R Notebook
library(dplyr)
library(tidyr)
library(Rmisc)
library(lubridate)
library(ggplot2)
library(car)
library(MASS)
library(mgcv)
library(MuMIn)
library(emmeans)
library(ggrepel)
library(effects)
library(lme4)
library(nlme)
library(sjPlot)
library(drc)
library(scales)
library(xfun)#KBay pairs physiology
phys<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Phys data for R with Teegan no Oct-Nov 2020 and only peak bleaching.csv", strip.white=T)
phys$Date<- as.Date(phys$Date, format = "%Y-%m-%d")
phys$Bleach<-as.factor(phys$Bleach)
phys$Months<-as.factor(phys$Months)
phys$Species<-as.factor(phys$Species)
phys$Coral_ID<-as.factor(phys$Coral_ID)
physunique(phys$Months)[1] 10 12 17 20 24 29 35 0
Levels: 0 10 12 17 20 24 29 35phys_stress= filter(phys, Months %in% c("0","12","24","35"))
phys_stress##Endolothics
endolith<- glm(Endolithic ~ Species*Bleach*Months, data = phys, family = "binomial")
#summary(endolith)
car::Anova(endolith, type=3)Warning: glm.fit: fitted probabilities numerically 0 or 1 occurredAnalysis of Deviance Table (Type III tests)
Response: Endolithic
LR Chisq Df Pr(>Chisq)
Species 8.5104 1 0.003531 **
Bleach 0.0000 1 1.000000
Months 4.1128 5 0.533296
Species:Bleach 0.0000 1 0.999983
Species:Months 4.4367 5 0.488398
Bleach:Months 1.8132 5 0.874335
Species:Bleach:Months 1.2610 5 0.938894
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
endofig<-ggplot(phys, aes(y=Endolithic, x=Date, color=Bleach, fill=Bleach))+
geom_jitter()+
#geom_smooth(method="loess")+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Presence~of~endolithic~algae))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
#legend.position=c(0.15,0.85),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
endofig
##Protein ###Normality
hist(phys$Protein_mg.cm.2)
protein.lm<- lm(Protein_mg.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(protein.lm, ask=FALSE, which=1:6)
library(MuMIn)
summary(protein.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.04101892 0.09504707
Fixed effects: Protein_mg.cm.2 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.709
BleachNon-bleach -0.707 0.502
Months10 -0.585 0.415 0.414
Months12 -0.650 0.461 0.460 0.450
Months17 -0.650 0.461 0.460 0.450 0.500
Months20 -0.631 0.448 0.446 0.435 0.486 0.486
Months24 -0.631 0.448 0.446 0.442 0.485 0.485 0.471
Months29 -0.631 0.448 0.446 0.442 0.485 0.485 0.471 0.477
Months35 -0.496 0.352 0.351 0.329 0.366 0.366 0.358 0.359 0.359
SpeciesPorites compressa:BleachNon-bleach 0.503 -0.705 -0.711 -0.294 -0.327 -0.327 -0.317 -0.317 -0.317 -0.249
SpeciesPorites compressa:Months10 0.422 -0.598 -0.298 -0.721 -0.325 -0.325 -0.314 -0.319 -0.319 -0.237 0.424
SpeciesPorites compressa:Months12 0.452 -0.642 -0.320 -0.313 -0.696 -0.348 -0.338 -0.338 -0.338 -0.255 0.456 0.456
SpeciesPorites compressa:Months17 0.444 -0.630 -0.314 -0.308 -0.342 -0.684 -0.332 -0.332 -0.332 -0.250 0.446 0.450
SpeciesPorites compressa:Months20 0.446 -0.633 -0.315 -0.307 -0.343 -0.343 -0.706 -0.332 -0.332 -0.253 0.449 0.448
SpeciesPorites compressa:Months24 0.428 -0.613 -0.302 -0.300 -0.329 -0.329 -0.319 -0.678 -0.323 -0.243 0.439 0.432
SpeciesPorites compressa:Months29 0.437 -0.626 -0.309 -0.306 -0.336 -0.336 -0.326 -0.330 -0.693 -0.248 0.447 0.442
SpeciesPorites compressa:Months35 0.382 -0.542 -0.270 -0.253 -0.282 -0.282 -0.276 -0.276 -0.276 -0.770 0.383 0.370
BleachNon-bleach:Months10 0.429 -0.304 -0.607 -0.733 -0.330 -0.330 -0.319 -0.324 -0.324 -0.241 0.431 0.529
BleachNon-bleach:Months12 0.460 -0.326 -0.650 -0.318 -0.707 -0.354 -0.343 -0.343 -0.343 -0.259 0.462 0.229
BleachNon-bleach:Months17 0.460 -0.326 -0.650 -0.318 -0.354 -0.707 -0.343 -0.343 -0.343 -0.259 0.462 0.229
BleachNon-bleach:Months20 0.453 -0.321 -0.640 -0.312 -0.348 -0.348 -0.717 -0.338 -0.338 -0.257 0.455 0.225
BleachNon-bleach:Months24 0.446 -0.316 -0.631 -0.313 -0.343 -0.343 -0.333 -0.707 -0.337 -0.254 0.449 0.225
BleachNon-bleach:Months29 0.446 -0.316 -0.631 -0.313 -0.343 -0.343 -0.333 -0.337 -0.707 -0.254 0.449 0.225
BleachNon-bleach:Months35 0.383 -0.272 -0.537 -0.254 -0.283 -0.283 -0.277 -0.277 -0.277 -0.773 0.382 0.183
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.308 0.440 0.435 0.526 0.237 0.237 0.229 0.233 0.233 0.173 -0.624 -0.731
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.320 0.454 0.452 0.222 0.492 0.246 0.239 0.239 0.239 0.180 -0.644 -0.322
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.319 0.455 0.451 0.221 0.245 0.490 0.238 0.238 0.238 0.180 -0.645 -0.324
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.318 0.451 0.449 0.219 0.244 0.244 0.503 0.237 0.237 0.180 -0.640 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.302 0.437 0.426 0.211 0.232 0.232 0.225 0.478 0.228 0.171 -0.619 -0.304
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.308 0.445 0.436 0.216 0.237 0.237 0.230 0.233 0.489 0.175 -0.631 -0.311
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.278 0.395 0.389 0.184 0.205 0.205 0.201 0.201 0.201 0.560 -0.551 -0.269
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.480
SpeciesPorites compressa:Months20 0.482 0.473
SpeciesPorites compressa:Months24 0.461 0.452 0.454
SpeciesPorites compressa:Months29 0.472 0.462 0.465 0.457
SpeciesPorites compressa:Months35 0.395 0.390 0.391 0.378 0.387
BleachNon-bleach:Months10 0.230 0.226 0.225 0.220 0.225 0.186
BleachNon-bleach:Months12 0.492 0.242 0.243 0.233 0.238 0.199 0.467
BleachNon-bleach:Months17 0.246 0.483 0.243 0.233 0.238 0.199 0.467 0.500
BleachNon-bleach:Months20 0.242 0.238 0.507 0.229 0.234 0.198 0.459 0.493 0.493
BleachNon-bleach:Months24 0.239 0.235 0.235 0.479 0.233 0.195 0.458 0.485 0.485 0.478
BleachNon-bleach:Months29 0.239 0.235 0.235 0.228 0.490 0.195 0.458 0.485 0.485 0.478 0.477
BleachNon-bleach:Months35 0.197 0.194 0.196 0.188 0.192 0.596 0.375 0.400 0.400 0.396 0.392
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.332 -0.330 -0.327 -0.314 -0.322 -0.271 -0.718 -0.335 -0.335 -0.329 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.707 -0.339 -0.341 -0.326 -0.333 -0.280 -0.325 -0.696 -0.348 -0.343 -0.338
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.344 -0.718 -0.339 -0.323 -0.331 -0.281 -0.324 -0.347 -0.693 -0.342 -0.337
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.343 -0.337 -0.712 -0.323 -0.331 -0.279 -0.322 -0.345 -0.345 -0.701 -0.335
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.325 -0.318 -0.320 -0.709 -0.326 -0.268 -0.310 -0.328 -0.328 -0.323 -0.676
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.332 -0.326 -0.327 -0.326 -0.709 -0.275 -0.317 -0.335 -0.335 -0.330 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.287 -0.283 -0.284 -0.273 -0.280 -0.727 -0.272 -0.290 -0.290 -0.287 -0.284
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.392
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.329 -0.269
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.338 -0.279 0.470
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.337 -0.278 0.473 0.487
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.335 -0.278 0.466 0.485 0.483
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 -0.265 0.444 0.460 0.457 0.456
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.691 -0.271 0.455 0.470 0.468 0.467 0.460
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.284 -0.724 0.394 0.407 0.407 0.405 0.386 0.396
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-3.81584447 -0.53123873 -0.06830697 0.49705007 2.72119327
Number of Observations: 276
Number of Groups: 44 r.squaredGLMM(protein.lme) R2m R2c
[1,] 0.5506146 0.6211707#coef(protein.lme)###Stats
protein.lme <- lme(Protein_mg.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(protein.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Protein_mg.cm.2
Chisq Df Pr(>Chisq)
(Intercept) 28.0172 1 1.202e-07 ***
Species 7.1503 1 0.007495 **
Bleach 0.1095 1 0.740747
Months 46.2291 7 7.889e-08 ***
Species:Bleach 0.1174 1 0.731906
Species:Months 20.5300 7 0.004532 **
Bleach:Months 6.3841 7 0.495677
Species:Bleach:Months 8.2744 7 0.309023
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(protein.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Species")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 0.165 0.0231 43 0.119 0.212
Porites compressa 0 0.278 0.0231 42 0.231 0.324
Montipora capitata 10 0.299 0.0258 43 0.247 0.351
Porites compressa 10 0.359 0.0245 42 0.309 0.408
Montipora capitata 12 0.265 0.0231 43 0.218 0.311
Porites compressa 12 0.388 0.0243 42 0.339 0.437
Montipora capitata 17 0.256 0.0231 43 0.209 0.302
Porites compressa 17 0.525 0.0245 42 0.475 0.574
Montipora capitata 20 0.304 0.0237 43 0.256 0.352
Porites compressa 20 0.495 0.0243 42 0.446 0.545
Montipora capitata 24 0.341 0.0243 43 0.292 0.390
Porites compressa 24 0.521 0.0274 42 0.465 0.576
Montipora capitata 29 0.410 0.0243 43 0.361 0.459
Porites compressa 29 0.509 0.0257 42 0.457 0.561
Montipora capitata 35 0.469 0.0318 43 0.405 0.533
Porites compressa 35 0.443 0.0298 42 0.383 0.503
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Months`
Months = 0:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.1121 0.0327 42 -3.429 0.0014
Months = 10:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.0597 0.0356 42 -1.676 0.1012
Months = 12:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.1231 0.0336 42 -3.667 0.0007
Months = 17:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.2691 0.0337 42 -7.990 <.0001
Months = 20:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.1917 0.0340 42 -5.641 <.0001
Months = 24:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.1798 0.0366 42 -4.913 <.0001
Months = 29:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.0989 0.0354 42 -2.795 0.0078
Months = 35:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.0265 0.0435 42 0.608 0.5467
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment summary(protein.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.04101892 0.09504707
Fixed effects: Protein_mg.cm.2 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.709
BleachNon-bleach -0.707 0.502
Months10 -0.585 0.415 0.414
Months12 -0.650 0.461 0.460 0.450
Months17 -0.650 0.461 0.460 0.450 0.500
Months20 -0.631 0.448 0.446 0.435 0.486 0.486
Months24 -0.631 0.448 0.446 0.442 0.485 0.485 0.471
Months29 -0.631 0.448 0.446 0.442 0.485 0.485 0.471 0.477
Months35 -0.496 0.352 0.351 0.329 0.366 0.366 0.358 0.359 0.359
SpeciesPorites compressa:BleachNon-bleach 0.503 -0.705 -0.711 -0.294 -0.327 -0.327 -0.317 -0.317 -0.317 -0.249
SpeciesPorites compressa:Months10 0.422 -0.598 -0.298 -0.721 -0.325 -0.325 -0.314 -0.319 -0.319 -0.237 0.424
SpeciesPorites compressa:Months12 0.452 -0.642 -0.320 -0.313 -0.696 -0.348 -0.338 -0.338 -0.338 -0.255 0.456 0.456
SpeciesPorites compressa:Months17 0.444 -0.630 -0.314 -0.308 -0.342 -0.684 -0.332 -0.332 -0.332 -0.250 0.446 0.450
SpeciesPorites compressa:Months20 0.446 -0.633 -0.315 -0.307 -0.343 -0.343 -0.706 -0.332 -0.332 -0.253 0.449 0.448
SpeciesPorites compressa:Months24 0.428 -0.613 -0.302 -0.300 -0.329 -0.329 -0.319 -0.678 -0.323 -0.243 0.439 0.432
SpeciesPorites compressa:Months29 0.437 -0.626 -0.309 -0.306 -0.336 -0.336 -0.326 -0.330 -0.693 -0.248 0.447 0.442
SpeciesPorites compressa:Months35 0.382 -0.542 -0.270 -0.253 -0.282 -0.282 -0.276 -0.276 -0.276 -0.770 0.383 0.370
BleachNon-bleach:Months10 0.429 -0.304 -0.607 -0.733 -0.330 -0.330 -0.319 -0.324 -0.324 -0.241 0.431 0.529
BleachNon-bleach:Months12 0.460 -0.326 -0.650 -0.318 -0.707 -0.354 -0.343 -0.343 -0.343 -0.259 0.462 0.229
BleachNon-bleach:Months17 0.460 -0.326 -0.650 -0.318 -0.354 -0.707 -0.343 -0.343 -0.343 -0.259 0.462 0.229
BleachNon-bleach:Months20 0.453 -0.321 -0.640 -0.312 -0.348 -0.348 -0.717 -0.338 -0.338 -0.257 0.455 0.225
BleachNon-bleach:Months24 0.446 -0.316 -0.631 -0.313 -0.343 -0.343 -0.333 -0.707 -0.337 -0.254 0.449 0.225
BleachNon-bleach:Months29 0.446 -0.316 -0.631 -0.313 -0.343 -0.343 -0.333 -0.337 -0.707 -0.254 0.449 0.225
BleachNon-bleach:Months35 0.383 -0.272 -0.537 -0.254 -0.283 -0.283 -0.277 -0.277 -0.277 -0.773 0.382 0.183
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.308 0.440 0.435 0.526 0.237 0.237 0.229 0.233 0.233 0.173 -0.624 -0.731
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.320 0.454 0.452 0.222 0.492 0.246 0.239 0.239 0.239 0.180 -0.644 -0.322
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.319 0.455 0.451 0.221 0.245 0.490 0.238 0.238 0.238 0.180 -0.645 -0.324
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.318 0.451 0.449 0.219 0.244 0.244 0.503 0.237 0.237 0.180 -0.640 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.302 0.437 0.426 0.211 0.232 0.232 0.225 0.478 0.228 0.171 -0.619 -0.304
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.308 0.445 0.436 0.216 0.237 0.237 0.230 0.233 0.489 0.175 -0.631 -0.311
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.278 0.395 0.389 0.184 0.205 0.205 0.201 0.201 0.201 0.560 -0.551 -0.269
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.480
SpeciesPorites compressa:Months20 0.482 0.473
SpeciesPorites compressa:Months24 0.461 0.452 0.454
SpeciesPorites compressa:Months29 0.472 0.462 0.465 0.457
SpeciesPorites compressa:Months35 0.395 0.390 0.391 0.378 0.387
BleachNon-bleach:Months10 0.230 0.226 0.225 0.220 0.225 0.186
BleachNon-bleach:Months12 0.492 0.242 0.243 0.233 0.238 0.199 0.467
BleachNon-bleach:Months17 0.246 0.483 0.243 0.233 0.238 0.199 0.467 0.500
BleachNon-bleach:Months20 0.242 0.238 0.507 0.229 0.234 0.198 0.459 0.493 0.493
BleachNon-bleach:Months24 0.239 0.235 0.235 0.479 0.233 0.195 0.458 0.485 0.485 0.478
BleachNon-bleach:Months29 0.239 0.235 0.235 0.228 0.490 0.195 0.458 0.485 0.485 0.478 0.477
BleachNon-bleach:Months35 0.197 0.194 0.196 0.188 0.192 0.596 0.375 0.400 0.400 0.396 0.392
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.332 -0.330 -0.327 -0.314 -0.322 -0.271 -0.718 -0.335 -0.335 -0.329 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.707 -0.339 -0.341 -0.326 -0.333 -0.280 -0.325 -0.696 -0.348 -0.343 -0.338
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.344 -0.718 -0.339 -0.323 -0.331 -0.281 -0.324 -0.347 -0.693 -0.342 -0.337
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.343 -0.337 -0.712 -0.323 -0.331 -0.279 -0.322 -0.345 -0.345 -0.701 -0.335
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.325 -0.318 -0.320 -0.709 -0.326 -0.268 -0.310 -0.328 -0.328 -0.323 -0.676
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.332 -0.326 -0.327 -0.326 -0.709 -0.275 -0.317 -0.335 -0.335 -0.330 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.287 -0.283 -0.284 -0.273 -0.280 -0.727 -0.272 -0.290 -0.290 -0.287 -0.284
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.392
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.329 -0.269
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.338 -0.279 0.470
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.337 -0.278 0.473 0.487
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.335 -0.278 0.466 0.485 0.483
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 -0.265 0.444 0.460 0.457 0.456
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.691 -0.271 0.455 0.470 0.468 0.467 0.460
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.284 -0.724 0.394 0.407 0.407 0.405 0.386 0.396
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-3.81584447 -0.53123873 -0.06830697 0.49705007 2.72119327
Number of Observations: 276
Number of Groups: 44 r.squaredGLMM(protein.lme) R2m R2c
[1,] 0.5506146 0.6211707coef(protein.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 0.1759040 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
4 0.2218443 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
11 0.1824086 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
12 0.1432800 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
19 0.1650566 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
20 0.1370136 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
26 0.1585332 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
27 0.1552725 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
35 0.1759826 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
36 0.1632939 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
41 0.2291232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
42 0.1574232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
43 0.1611075 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
44 0.1136417 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
45 0.2021523 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
46 0.1381121 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
201 0.1377209 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
202 0.1370790 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
203 0.1878345 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
204 0.1747205 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
209 0.1539102 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
210 0.1453911 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
211 0.1763872 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
212 0.2245608 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
213 0.1717698 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
214 0.1646707 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
217 0.1835225 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
218 0.1927358 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
219 0.1975645 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
220 0.1905783 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
221 0.1721688 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 -0.02228106 -0.03772763 -0.02605817
4 -0.02228106 -0.03772763 -0.02605817
11 -0.02228106 -0.03772763 -0.02605817
12 -0.02228106 -0.03772763 -0.02605817
19 -0.02228106 -0.03772763 -0.02605817
20 -0.02228106 -0.03772763 -0.02605817
26 -0.02228106 -0.03772763 -0.02605817
27 -0.02228106 -0.03772763 -0.02605817
35 -0.02228106 -0.03772763 -0.02605817
36 -0.02228106 -0.03772763 -0.02605817
41 -0.02228106 -0.03772763 -0.02605817
42 -0.02228106 -0.03772763 -0.02605817
43 -0.02228106 -0.03772763 -0.02605817
44 -0.02228106 -0.03772763 -0.02605817
45 -0.02228106 -0.03772763 -0.02605817
46 -0.02228106 -0.03772763 -0.02605817
201 -0.02228106 -0.03772763 -0.02605817
202 -0.02228106 -0.03772763 -0.02605817
203 -0.02228106 -0.03772763 -0.02605817
204 -0.02228106 -0.03772763 -0.02605817
209 -0.02228106 -0.03772763 -0.02605817
210 -0.02228106 -0.03772763 -0.02605817
211 -0.02228106 -0.03772763 -0.02605817
212 -0.02228106 -0.03772763 -0.02605817
213 -0.02228106 -0.03772763 -0.02605817
214 -0.02228106 -0.03772763 -0.02605817
217 -0.02228106 -0.03772763 -0.02605817
218 -0.02228106 -0.03772763 -0.02605817
219 -0.02228106 -0.03772763 -0.02605817
220 -0.02228106 -0.03772763 -0.02605817
221 -0.02228106 -0.03772763 -0.02605817
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 0.1174555 0.0586134 0.0903154 0.04990827
4 0.1174555 0.0586134 0.0903154 0.04990827
11 0.1174555 0.0586134 0.0903154 0.04990827
12 0.1174555 0.0586134 0.0903154 0.04990827
19 0.1174555 0.0586134 0.0903154 0.04990827
20 0.1174555 0.0586134 0.0903154 0.04990827
26 0.1174555 0.0586134 0.0903154 0.04990827
27 0.1174555 0.0586134 0.0903154 0.04990827
35 0.1174555 0.0586134 0.0903154 0.04990827
36 0.1174555 0.0586134 0.0903154 0.04990827
41 0.1174555 0.0586134 0.0903154 0.04990827
42 0.1174555 0.0586134 0.0903154 0.04990827
43 0.1174555 0.0586134 0.0903154 0.04990827
44 0.1174555 0.0586134 0.0903154 0.04990827
45 0.1174555 0.0586134 0.0903154 0.04990827
46 0.1174555 0.0586134 0.0903154 0.04990827
201 0.1174555 0.0586134 0.0903154 0.04990827
202 0.1174555 0.0586134 0.0903154 0.04990827
203 0.1174555 0.0586134 0.0903154 0.04990827
204 0.1174555 0.0586134 0.0903154 0.04990827
209 0.1174555 0.0586134 0.0903154 0.04990827
210 0.1174555 0.0586134 0.0903154 0.04990827
211 0.1174555 0.0586134 0.0903154 0.04990827
212 0.1174555 0.0586134 0.0903154 0.04990827
213 0.1174555 0.0586134 0.0903154 0.04990827
214 0.1174555 0.0586134 0.0903154 0.04990827
217 0.1174555 0.0586134 0.0903154 0.04990827
218 0.1174555 0.0586134 0.0903154 0.04990827
219 0.1174555 0.0586134 0.0903154 0.04990827
220 0.1174555 0.0586134 0.0903154 0.04990827
221 0.1174555 0.0586134 0.0903154 0.04990827
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
4 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
11 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
12 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
19 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
20 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
26 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
27 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
35 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
36 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
41 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
42 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
43 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
44 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
45 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
46 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
201 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
202 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
203 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
204 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
209 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
210 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
211 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
212 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
213 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
214 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
217 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
218 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
219 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
220 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
221 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 0.08454026 0.05176502 0.03536143 -0.02947219
4 0.08454026 0.05176502 0.03536143 -0.02947219
11 0.08454026 0.05176502 0.03536143 -0.02947219
12 0.08454026 0.05176502 0.03536143 -0.02947219
19 0.08454026 0.05176502 0.03536143 -0.02947219
20 0.08454026 0.05176502 0.03536143 -0.02947219
26 0.08454026 0.05176502 0.03536143 -0.02947219
27 0.08454026 0.05176502 0.03536143 -0.02947219
35 0.08454026 0.05176502 0.03536143 -0.02947219
36 0.08454026 0.05176502 0.03536143 -0.02947219
41 0.08454026 0.05176502 0.03536143 -0.02947219
42 0.08454026 0.05176502 0.03536143 -0.02947219
43 0.08454026 0.05176502 0.03536143 -0.02947219
44 0.08454026 0.05176502 0.03536143 -0.02947219
45 0.08454026 0.05176502 0.03536143 -0.02947219
46 0.08454026 0.05176502 0.03536143 -0.02947219
201 0.08454026 0.05176502 0.03536143 -0.02947219
202 0.08454026 0.05176502 0.03536143 -0.02947219
203 0.08454026 0.05176502 0.03536143 -0.02947219
204 0.08454026 0.05176502 0.03536143 -0.02947219
209 0.08454026 0.05176502 0.03536143 -0.02947219
210 0.08454026 0.05176502 0.03536143 -0.02947219
211 0.08454026 0.05176502 0.03536143 -0.02947219
212 0.08454026 0.05176502 0.03536143 -0.02947219
213 0.08454026 0.05176502 0.03536143 -0.02947219
214 0.08454026 0.05176502 0.03536143 -0.02947219
217 0.08454026 0.05176502 0.03536143 -0.02947219
218 0.08454026 0.05176502 0.03536143 -0.02947219
219 0.08454026 0.05176502 0.03536143 -0.02947219
220 0.08454026 0.05176502 0.03536143 -0.02947219
221 0.08454026 0.05176502 0.03536143 -0.02947219
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 0.07407306 0.07902784
4 0.07407306 0.07902784
11 0.07407306 0.07902784
12 0.07407306 0.07902784
19 0.07407306 0.07902784
20 0.07407306 0.07902784
26 0.07407306 0.07902784
27 0.07407306 0.07902784
35 0.07407306 0.07902784
36 0.07407306 0.07902784
41 0.07407306 0.07902784
42 0.07407306 0.07902784
43 0.07407306 0.07902784
44 0.07407306 0.07902784
45 0.07407306 0.07902784
46 0.07407306 0.07902784
201 0.07407306 0.07902784
202 0.07407306 0.07902784
203 0.07407306 0.07902784
204 0.07407306 0.07902784
209 0.07407306 0.07902784
210 0.07407306 0.07902784
211 0.07407306 0.07902784
212 0.07407306 0.07902784
213 0.07407306 0.07902784
214 0.07407306 0.07902784
217 0.07407306 0.07902784
218 0.07407306 0.07902784
219 0.07407306 0.07902784
220 0.07407306 0.07902784
221 0.07407306 0.07902784
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 0.04188296 -0.04538026
4 0.04188296 -0.04538026
11 0.04188296 -0.04538026
12 0.04188296 -0.04538026
19 0.04188296 -0.04538026
20 0.04188296 -0.04538026
26 0.04188296 -0.04538026
27 0.04188296 -0.04538026
35 0.04188296 -0.04538026
36 0.04188296 -0.04538026
41 0.04188296 -0.04538026
42 0.04188296 -0.04538026
43 0.04188296 -0.04538026
44 0.04188296 -0.04538026
45 0.04188296 -0.04538026
46 0.04188296 -0.04538026
201 0.04188296 -0.04538026
202 0.04188296 -0.04538026
203 0.04188296 -0.04538026
204 0.04188296 -0.04538026
209 0.04188296 -0.04538026
210 0.04188296 -0.04538026
211 0.04188296 -0.04538026
212 0.04188296 -0.04538026
213 0.04188296 -0.04538026
214 0.04188296 -0.04538026
217 0.04188296 -0.04538026
218 0.04188296 -0.04538026
219 0.04188296 -0.04538026
220 0.04188296 -0.04538026
221 0.04188296 -0.04538026
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.1263666 0.07181537
4 -0.1263666 0.07181537
11 -0.1263666 0.07181537
12 -0.1263666 0.07181537
19 -0.1263666 0.07181537
20 -0.1263666 0.07181537
26 -0.1263666 0.07181537
27 -0.1263666 0.07181537
35 -0.1263666 0.07181537
36 -0.1263666 0.07181537
41 -0.1263666 0.07181537
42 -0.1263666 0.07181537
43 -0.1263666 0.07181537
44 -0.1263666 0.07181537
45 -0.1263666 0.07181537
46 -0.1263666 0.07181537
201 -0.1263666 0.07181537
202 -0.1263666 0.07181537
203 -0.1263666 0.07181537
204 -0.1263666 0.07181537
209 -0.1263666 0.07181537
210 -0.1263666 0.07181537
211 -0.1263666 0.07181537
212 -0.1263666 0.07181537
213 -0.1263666 0.07181537
214 -0.1263666 0.07181537
217 -0.1263666 0.07181537
218 -0.1263666 0.07181537
219 -0.1263666 0.07181537
220 -0.1263666 0.07181537
221 -0.1263666 0.07181537
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]####Coefficients
coef(protein.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 0.1759040 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
4 0.2218443 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
11 0.1824086 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
12 0.1432800 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
19 0.1650566 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
20 0.1370136 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
26 0.1585332 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
27 0.1552725 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
35 0.1759826 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
36 0.1632939 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
41 0.2291232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
42 0.1574232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
43 0.1611075 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
44 0.1136417 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
45 0.2021523 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
46 0.1381121 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
201 0.1377209 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
202 0.1370790 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
203 0.1878345 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
204 0.1747205 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
209 0.1539102 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
210 0.1453911 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
211 0.1763872 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
212 0.2245608 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
213 0.1717698 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
214 0.1646707 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
217 0.1835225 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
218 0.1927358 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
219 0.1975645 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
220 0.1905783 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
221 0.1721688 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 -0.02228106 -0.03772763 -0.02605817
4 -0.02228106 -0.03772763 -0.02605817
11 -0.02228106 -0.03772763 -0.02605817
12 -0.02228106 -0.03772763 -0.02605817
19 -0.02228106 -0.03772763 -0.02605817
20 -0.02228106 -0.03772763 -0.02605817
26 -0.02228106 -0.03772763 -0.02605817
27 -0.02228106 -0.03772763 -0.02605817
35 -0.02228106 -0.03772763 -0.02605817
36 -0.02228106 -0.03772763 -0.02605817
41 -0.02228106 -0.03772763 -0.02605817
42 -0.02228106 -0.03772763 -0.02605817
43 -0.02228106 -0.03772763 -0.02605817
44 -0.02228106 -0.03772763 -0.02605817
45 -0.02228106 -0.03772763 -0.02605817
46 -0.02228106 -0.03772763 -0.02605817
201 -0.02228106 -0.03772763 -0.02605817
202 -0.02228106 -0.03772763 -0.02605817
203 -0.02228106 -0.03772763 -0.02605817
204 -0.02228106 -0.03772763 -0.02605817
209 -0.02228106 -0.03772763 -0.02605817
210 -0.02228106 -0.03772763 -0.02605817
211 -0.02228106 -0.03772763 -0.02605817
212 -0.02228106 -0.03772763 -0.02605817
213 -0.02228106 -0.03772763 -0.02605817
214 -0.02228106 -0.03772763 -0.02605817
217 -0.02228106 -0.03772763 -0.02605817
218 -0.02228106 -0.03772763 -0.02605817
219 -0.02228106 -0.03772763 -0.02605817
220 -0.02228106 -0.03772763 -0.02605817
221 -0.02228106 -0.03772763 -0.02605817
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 0.1174555 0.0586134 0.0903154 0.04990827
4 0.1174555 0.0586134 0.0903154 0.04990827
11 0.1174555 0.0586134 0.0903154 0.04990827
12 0.1174555 0.0586134 0.0903154 0.04990827
19 0.1174555 0.0586134 0.0903154 0.04990827
20 0.1174555 0.0586134 0.0903154 0.04990827
26 0.1174555 0.0586134 0.0903154 0.04990827
27 0.1174555 0.0586134 0.0903154 0.04990827
35 0.1174555 0.0586134 0.0903154 0.04990827
36 0.1174555 0.0586134 0.0903154 0.04990827
41 0.1174555 0.0586134 0.0903154 0.04990827
42 0.1174555 0.0586134 0.0903154 0.04990827
43 0.1174555 0.0586134 0.0903154 0.04990827
44 0.1174555 0.0586134 0.0903154 0.04990827
45 0.1174555 0.0586134 0.0903154 0.04990827
46 0.1174555 0.0586134 0.0903154 0.04990827
201 0.1174555 0.0586134 0.0903154 0.04990827
202 0.1174555 0.0586134 0.0903154 0.04990827
203 0.1174555 0.0586134 0.0903154 0.04990827
204 0.1174555 0.0586134 0.0903154 0.04990827
209 0.1174555 0.0586134 0.0903154 0.04990827
210 0.1174555 0.0586134 0.0903154 0.04990827
211 0.1174555 0.0586134 0.0903154 0.04990827
212 0.1174555 0.0586134 0.0903154 0.04990827
213 0.1174555 0.0586134 0.0903154 0.04990827
214 0.1174555 0.0586134 0.0903154 0.04990827
217 0.1174555 0.0586134 0.0903154 0.04990827
218 0.1174555 0.0586134 0.0903154 0.04990827
219 0.1174555 0.0586134 0.0903154 0.04990827
220 0.1174555 0.0586134 0.0903154 0.04990827
221 0.1174555 0.0586134 0.0903154 0.04990827
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
4 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
11 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
12 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
19 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
20 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
26 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
27 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
35 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
36 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
41 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
42 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
43 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
44 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
45 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
46 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
201 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
202 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
203 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
204 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
209 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
210 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
211 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
212 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
213 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
214 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
217 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
218 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
219 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
220 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
221 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 0.08454026 0.05176502 0.03536143 -0.02947219
4 0.08454026 0.05176502 0.03536143 -0.02947219
11 0.08454026 0.05176502 0.03536143 -0.02947219
12 0.08454026 0.05176502 0.03536143 -0.02947219
19 0.08454026 0.05176502 0.03536143 -0.02947219
20 0.08454026 0.05176502 0.03536143 -0.02947219
26 0.08454026 0.05176502 0.03536143 -0.02947219
27 0.08454026 0.05176502 0.03536143 -0.02947219
35 0.08454026 0.05176502 0.03536143 -0.02947219
36 0.08454026 0.05176502 0.03536143 -0.02947219
41 0.08454026 0.05176502 0.03536143 -0.02947219
42 0.08454026 0.05176502 0.03536143 -0.02947219
43 0.08454026 0.05176502 0.03536143 -0.02947219
44 0.08454026 0.05176502 0.03536143 -0.02947219
45 0.08454026 0.05176502 0.03536143 -0.02947219
46 0.08454026 0.05176502 0.03536143 -0.02947219
201 0.08454026 0.05176502 0.03536143 -0.02947219
202 0.08454026 0.05176502 0.03536143 -0.02947219
203 0.08454026 0.05176502 0.03536143 -0.02947219
204 0.08454026 0.05176502 0.03536143 -0.02947219
209 0.08454026 0.05176502 0.03536143 -0.02947219
210 0.08454026 0.05176502 0.03536143 -0.02947219
211 0.08454026 0.05176502 0.03536143 -0.02947219
212 0.08454026 0.05176502 0.03536143 -0.02947219
213 0.08454026 0.05176502 0.03536143 -0.02947219
214 0.08454026 0.05176502 0.03536143 -0.02947219
217 0.08454026 0.05176502 0.03536143 -0.02947219
218 0.08454026 0.05176502 0.03536143 -0.02947219
219 0.08454026 0.05176502 0.03536143 -0.02947219
220 0.08454026 0.05176502 0.03536143 -0.02947219
221 0.08454026 0.05176502 0.03536143 -0.02947219
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 0.07407306 0.07902784
4 0.07407306 0.07902784
11 0.07407306 0.07902784
12 0.07407306 0.07902784
19 0.07407306 0.07902784
20 0.07407306 0.07902784
26 0.07407306 0.07902784
27 0.07407306 0.07902784
35 0.07407306 0.07902784
36 0.07407306 0.07902784
41 0.07407306 0.07902784
42 0.07407306 0.07902784
43 0.07407306 0.07902784
44 0.07407306 0.07902784
45 0.07407306 0.07902784
46 0.07407306 0.07902784
201 0.07407306 0.07902784
202 0.07407306 0.07902784
203 0.07407306 0.07902784
204 0.07407306 0.07902784
209 0.07407306 0.07902784
210 0.07407306 0.07902784
211 0.07407306 0.07902784
212 0.07407306 0.07902784
213 0.07407306 0.07902784
214 0.07407306 0.07902784
217 0.07407306 0.07902784
218 0.07407306 0.07902784
219 0.07407306 0.07902784
220 0.07407306 0.07902784
221 0.07407306 0.07902784
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 0.04188296 -0.04538026
4 0.04188296 -0.04538026
11 0.04188296 -0.04538026
12 0.04188296 -0.04538026
19 0.04188296 -0.04538026
20 0.04188296 -0.04538026
26 0.04188296 -0.04538026
27 0.04188296 -0.04538026
35 0.04188296 -0.04538026
36 0.04188296 -0.04538026
41 0.04188296 -0.04538026
42 0.04188296 -0.04538026
43 0.04188296 -0.04538026
44 0.04188296 -0.04538026
45 0.04188296 -0.04538026
46 0.04188296 -0.04538026
201 0.04188296 -0.04538026
202 0.04188296 -0.04538026
203 0.04188296 -0.04538026
204 0.04188296 -0.04538026
209 0.04188296 -0.04538026
210 0.04188296 -0.04538026
211 0.04188296 -0.04538026
212 0.04188296 -0.04538026
213 0.04188296 -0.04538026
214 0.04188296 -0.04538026
217 0.04188296 -0.04538026
218 0.04188296 -0.04538026
219 0.04188296 -0.04538026
220 0.04188296 -0.04538026
221 0.04188296 -0.04538026
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.1263666 0.07181537
4 -0.1263666 0.07181537
11 -0.1263666 0.07181537
12 -0.1263666 0.07181537
19 -0.1263666 0.07181537
20 -0.1263666 0.07181537
26 -0.1263666 0.07181537
27 -0.1263666 0.07181537
35 -0.1263666 0.07181537
36 -0.1263666 0.07181537
41 -0.1263666 0.07181537
42 -0.1263666 0.07181537
43 -0.1263666 0.07181537
44 -0.1263666 0.07181537
45 -0.1263666 0.07181537
46 -0.1263666 0.07181537
201 -0.1263666 0.07181537
202 -0.1263666 0.07181537
203 -0.1263666 0.07181537
204 -0.1263666 0.07181537
209 -0.1263666 0.07181537
210 -0.1263666 0.07181537
211 -0.1263666 0.07181537
212 -0.1263666 0.07181537
213 -0.1263666 0.07181537
214 -0.1263666 0.07181537
217 -0.1263666 0.07181537
218 -0.1263666 0.07181537
219 -0.1263666 0.07181537
220 -0.1263666 0.07181537
221 -0.1263666 0.07181537
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]proteinavg<-summarySE(phys, measurevar='Protein_mg.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
proteinavg###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
proteinfig<-ggplot(phys, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %Y")+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
proteinfig
library(Rmisc)
protein_sum<-summarySE(phys, measurevar='Protein_mg.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
protein_sumproteinfig_3<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.8),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statproteinfig_3
proteinfig_2<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
#geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(date_breaks = "4 months", date_labels = "%b %Y")+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.8),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthproteinfig_2
proteinfig_3<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.8),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statproteinfig_3
library(Rmisc)
protein_stress<-summarySE(phys_stress, measurevar='Protein_mg.cm.2', groupvars=c('Months','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
protein_stressprotein_stress_fig<-ggplot(protein_stress, aes(y=Protein_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
facet_grid(~Species)+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
protein_stress_fig
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
protein_stress_fig2<-ggplot(protein_stress, aes(y=Protein_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+
#geom_boxplot(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
#geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
geom_point(size=1.5, position= pd)+
geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3))+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))Warning: Ignoring unknown aesthetics: statprotein_stress_fig2
##AFDW ###Normality
hist(phys$AFDW_mg.cm.2)
AFDW.lm<- lm(AFDW_mg.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(AFDW.lm, ask=FALSE, which=1:6)
###Stats
AFDW.lme <- lme(AFDW_mg.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(AFDW.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: AFDW_mg.cm.2
Chisq Df Pr(>Chisq)
(Intercept) 13.0317 1 0.0003063 ***
Species 7.9843 1 0.0047186 **
Bleach 0.0481 1 0.8264576
Months 92.5381 7 < 2.2e-16 ***
Species:Bleach 0.8137 1 0.3670394
Species:Months 15.9326 7 0.0257390 *
Bleach:Months 2.1034 7 0.9538982
Species:Bleach:Months 13.7309 7 0.0561806 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(AFDW.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 2.12 0.399 43 1.32 2.93
Porites compressa 0 3.87 0.399 42 3.06 4.67
Montipora capitata 10 7.30 0.449 43 6.40 8.21
Porites compressa 10 9.18 0.423 42 8.33 10.04
Montipora capitata 12 3.21 0.399 43 2.40 4.01
Porites compressa 12 5.04 0.420 42 4.19 5.89
Montipora capitata 17 5.83 0.399 43 5.03 6.63
Porites compressa 17 11.01 0.423 42 10.16 11.87
Montipora capitata 20 6.57 0.410 43 5.74 7.39
Porites compressa 20 10.35 0.420 42 9.50 11.20
Montipora capitata 24 4.59 0.433 43 3.71 5.46
Porites compressa 24 7.37 0.476 42 6.41 8.34
Montipora capitata 29 7.58 0.420 43 6.73 8.43
Porites compressa 29 9.77 0.446 42 8.87 10.67
Montipora capitata 35 7.57 0.558 43 6.45 8.70
Porites compressa 35 8.48 0.521 42 7.43 9.53
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months0 - Months10 -5.17825 0.590 201 -8.771 <.0001
Months0 - Months12 -1.08394 0.553 201 -1.960 0.5117
Months0 - Months17 -3.70793 0.553 201 -6.704 <.0001
Months0 - Months20 -4.44604 0.561 201 -7.926 <.0001
Months0 - Months24 -2.46392 0.578 201 -4.260 0.0008
Months0 - Months29 -5.45601 0.569 201 -9.593 <.0001
Months0 - Months35 -5.44798 0.679 201 -8.028 <.0001
Months10 - Months12 4.09431 0.590 201 6.935 <.0001
Months10 - Months17 1.47032 0.590 201 2.490 0.2056
Months10 - Months20 0.73220 0.598 201 1.224 0.9238
Months10 - Months24 2.71433 0.613 201 4.431 0.0004
Months10 - Months29 -0.27776 0.604 201 -0.460 0.9998
Months10 - Months35 -0.26973 0.709 201 -0.380 0.9999
Months12 - Months17 -2.62399 0.553 201 -4.744 0.0001
Months12 - Months20 -3.36211 0.561 201 -5.993 <.0001
Months12 - Months24 -1.37998 0.578 201 -2.386 0.2539
Months12 - Months29 -4.37207 0.569 201 -7.687 <.0001
Months12 - Months35 -4.36404 0.679 201 -6.431 <.0001
Months17 - Months20 -0.73811 0.561 201 -1.316 0.8920
Months17 - Months24 1.24401 0.578 201 2.151 0.3862
Months17 - Months29 -1.74808 0.569 201 -3.073 0.0486
Months17 - Months35 -1.74005 0.679 201 -2.564 0.1754
Months20 - Months24 1.98212 0.586 201 3.383 0.0192
Months20 - Months29 -1.00997 0.576 201 -1.752 0.6531
Months20 - Months35 -1.00193 0.685 201 -1.463 0.8259
Months24 - Months29 -2.99209 0.592 201 -5.051 <.0001
Months24 - Months35 -2.98406 0.699 201 -4.267 0.0008
Months29 - Months35 0.00804 0.691 201 0.012 1.0000
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months0 - Months10 -5.31725 0.571 201 -9.316 <.0001
Months0 - Months12 -1.17164 0.569 201 -2.060 0.4447
Months0 - Months17 -7.14605 0.571 201 -12.520 <.0001
Months0 - Months20 -6.48014 0.569 201 -11.392 <.0001
Months0 - Months24 -3.50771 0.611 201 -5.738 <.0001
Months0 - Months29 -5.90256 0.588 201 -10.042 <.0001
Months0 - Months35 -4.60996 0.648 201 -7.111 <.0001
Months10 - Months12 4.14561 0.585 201 7.088 <.0001
Months10 - Months17 -1.82880 0.587 201 -3.117 0.0428
Months10 - Months20 -1.16289 0.585 201 -1.988 0.4925
Months10 - Months24 1.80954 0.626 201 2.889 0.0802
Months10 - Months29 -0.58531 0.603 201 -0.970 0.9781
Months10 - Months35 0.70730 0.663 201 1.067 0.9628
Months12 - Months17 -5.97441 0.585 201 -10.214 <.0001
Months12 - Months20 -5.30850 0.583 201 -9.105 <.0001
Months12 - Months24 -2.33607 0.625 201 -3.741 0.0058
Months12 - Months29 -4.73092 0.602 201 -7.865 <.0001
Months12 - Months35 -3.43832 0.661 201 -5.202 <.0001
Months17 - Months20 0.66591 0.585 201 1.138 0.9475
Months17 - Months24 3.63834 0.626 201 5.809 <.0001
Months17 - Months29 1.24349 0.603 201 2.061 0.4440
Months17 - Months35 2.53610 0.663 201 3.827 0.0042
Months20 - Months24 2.97243 0.625 201 4.760 0.0001
Months20 - Months29 0.57758 0.602 201 0.960 0.9793
Months20 - Months35 1.87018 0.661 201 2.830 0.0935
Months24 - Months29 -2.39485 0.641 201 -3.738 0.0058
Months24 - Months35 -1.10225 0.698 201 -1.580 0.7617
Months29 - Months35 1.29260 0.676 201 1.911 0.5451
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 8 estimates summary(AFDW.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.3465371 1.749079
Fixed effects: AFDW_mg.cm.2 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.707
BleachNon-bleach -0.707 0.500
Months10 -0.628 0.444 0.444
Months12 -0.694 0.491 0.490 0.452
Months17 -0.694 0.491 0.490 0.452 0.500
Months20 -0.675 0.477 0.477 0.439 0.486 0.486
Months24 -0.653 0.462 0.462 0.429 0.471 0.471 0.457
Months29 -0.675 0.477 0.477 0.442 0.486 0.486 0.473 0.459
Months35 -0.524 0.371 0.371 0.338 0.374 0.374 0.365 0.351 0.365
SpeciesPorites compressa:BleachNon-bleach 0.500 -0.707 -0.707 -0.314 -0.347 -0.347 -0.337 -0.327 -0.337 -0.262
SpeciesPorites compressa:Months10 0.452 -0.640 -0.320 -0.721 -0.326 -0.326 -0.317 -0.309 -0.318 -0.244 0.453
SpeciesPorites compressa:Months12 0.484 -0.684 -0.342 -0.315 -0.697 -0.349 -0.339 -0.328 -0.339 -0.261 0.484 0.456
SpeciesPorites compressa:Months17 0.475 -0.672 -0.336 -0.310 -0.343 -0.685 -0.333 -0.322 -0.333 -0.257 0.475 0.449
SpeciesPorites compressa:Months20 0.477 -0.675 -0.337 -0.311 -0.344 -0.344 -0.707 -0.323 -0.334 -0.258 0.477 0.449
SpeciesPorites compressa:Months24 0.452 -0.641 -0.320 -0.297 -0.326 -0.326 -0.317 -0.692 -0.318 -0.243 0.455 0.427
SpeciesPorites compressa:Months29 0.469 -0.664 -0.331 -0.307 -0.338 -0.338 -0.328 -0.319 -0.695 -0.254 0.471 0.442
SpeciesPorites compressa:Months35 0.403 -0.571 -0.285 -0.260 -0.288 -0.288 -0.281 -0.270 -0.281 -0.769 0.404 0.377
BleachNon-bleach:Months10 0.460 -0.325 -0.650 -0.732 -0.331 -0.331 -0.322 -0.314 -0.323 -0.248 0.460 0.528
BleachNon-bleach:Months12 0.490 -0.347 -0.694 -0.320 -0.707 -0.354 -0.344 -0.333 -0.344 -0.265 0.491 0.231
BleachNon-bleach:Months17 0.490 -0.347 -0.694 -0.320 -0.354 -0.707 -0.344 -0.333 -0.344 -0.265 0.491 0.231
BleachNon-bleach:Months20 0.484 -0.342 -0.684 -0.315 -0.349 -0.349 -0.717 -0.328 -0.339 -0.262 0.484 0.227
BleachNon-bleach:Months24 0.469 -0.332 -0.663 -0.308 -0.338 -0.338 -0.329 -0.719 -0.330 -0.252 0.469 0.222
BleachNon-bleach:Months29 0.477 -0.337 -0.675 -0.312 -0.344 -0.344 -0.334 -0.325 -0.707 -0.258 0.477 0.225
BleachNon-bleach:Months35 0.404 -0.285 -0.570 -0.260 -0.288 -0.288 -0.281 -0.270 -0.281 -0.770 0.403 0.188
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.330 0.468 0.467 0.526 0.238 0.238 0.231 0.226 0.232 0.178 -0.662 -0.730
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.342 0.484 0.484 0.223 0.493 0.246 0.240 0.232 0.240 0.185 -0.684 -0.322
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.341 0.483 0.482 0.222 0.246 0.492 0.239 0.231 0.239 0.184 -0.684 -0.323
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.340 0.480 0.480 0.221 0.245 0.245 0.503 0.230 0.238 0.184 -0.679 -0.320
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 0.458 0.455 0.212 0.232 0.232 0.225 0.493 0.226 0.173 -0.647 -0.304
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.331 0.470 0.468 0.217 0.239 0.239 0.232 0.225 0.491 0.179 -0.665 -0.312
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.292 0.413 0.412 0.188 0.208 0.208 0.203 0.195 0.203 0.557 -0.582 -0.272
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.479
SpeciesPorites compressa:Months20 0.480 0.472
SpeciesPorites compressa:Months24 0.455 0.447 0.449
SpeciesPorites compressa:Months29 0.472 0.464 0.465 0.445
SpeciesPorites compressa:Months35 0.402 0.396 0.397 0.376 0.392
BleachNon-bleach:Months10 0.231 0.227 0.227 0.218 0.225 0.191
BleachNon-bleach:Months12 0.493 0.242 0.243 0.230 0.239 0.204 0.468
BleachNon-bleach:Months17 0.246 0.485 0.243 0.230 0.239 0.204 0.468 0.500
BleachNon-bleach:Months20 0.243 0.239 0.507 0.227 0.235 0.201 0.461 0.493 0.493
BleachNon-bleach:Months24 0.236 0.232 0.232 0.498 0.229 0.194 0.451 0.478 0.478 0.471
BleachNon-bleach:Months29 0.240 0.236 0.236 0.225 0.491 0.199 0.457 0.486 0.486 0.479 0.467
BleachNon-bleach:Months35 0.201 0.197 0.199 0.187 0.195 0.592 0.382 0.408 0.408 0.402 0.390
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.332 -0.328 -0.328 -0.311 -0.322 -0.275 -0.718 -0.337 -0.337 -0.332 -0.324
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.707 -0.339 -0.340 -0.322 -0.334 -0.284 -0.327 -0.697 -0.349 -0.344 -0.333
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.343 -0.718 -0.339 -0.320 -0.333 -0.284 -0.326 -0.348 -0.695 -0.343 -0.333
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.342 -0.336 -0.712 -0.319 -0.331 -0.283 -0.324 -0.346 -0.346 -0.702 -0.331
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.324 -0.318 -0.319 -0.713 -0.318 -0.268 -0.309 -0.328 -0.328 -0.323 -0.686
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.333 -0.327 -0.329 -0.316 -0.708 -0.277 -0.317 -0.338 -0.338 -0.333 -0.324
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.291 -0.286 -0.287 -0.272 -0.283 -0.724 -0.276 -0.295 -0.295 -0.291 -0.282
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.398
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.329 -0.275
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.339 -0.284 0.470
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.338 -0.283 0.471 0.486
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.337 -0.283 0.467 0.484 0.482
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.320 -0.267 0.443 0.458 0.457 0.455
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.694 -0.276 0.456 0.471 0.470 0.468 0.449
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.287 -0.723 0.398 0.412 0.411 0.409 0.387 0.400
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-4.477821768 -0.516104212 0.006458293 0.528053918 2.819238066
Number of Observations: 275
Number of Groups: 44 r.squaredGLMM(AFDW.lme) R2m R2c
[1,] 0.6918281 0.7034681####Coefficients
coef(AFDW.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 2.085664 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
4 2.032397 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
11 1.944082 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
12 2.049077 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
19 2.140051 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
20 2.037847 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
26 2.109987 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
27 2.007772 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
35 2.168458 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
36 1.990676 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
41 2.416779 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
42 2.229778 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
43 1.954513 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
44 1.845654 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
45 2.213627 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
46 1.675782 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
201 1.989219 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
202 2.121663 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
203 1.969132 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
204 2.069564 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
209 2.016175 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
210 2.144541 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
211 1.919986 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
212 2.117761 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
213 2.002797 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
214 2.063590 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
217 2.160648 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
218 2.038688 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
219 2.031608 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
220 1.909636 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
221 2.129944 2.252636 0.1748212 5.248146 0.9425809 3.64535 4.599669 2.021214 5.35493 5.908492
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 -1.016819 0.3821685 -1.047693
4 -1.016819 0.3821685 -1.047693
11 -1.016819 0.3821685 -1.047693
12 -1.016819 0.3821685 -1.047693
19 -1.016819 0.3821685 -1.047693
20 -1.016819 0.3821685 -1.047693
26 -1.016819 0.3821685 -1.047693
27 -1.016819 0.3821685 -1.047693
35 -1.016819 0.3821685 -1.047693
36 -1.016819 0.3821685 -1.047693
41 -1.016819 0.3821685 -1.047693
42 -1.016819 0.3821685 -1.047693
43 -1.016819 0.3821685 -1.047693
44 -1.016819 0.3821685 -1.047693
45 -1.016819 0.3821685 -1.047693
46 -1.016819 0.3821685 -1.047693
201 -1.016819 0.3821685 -1.047693
202 -1.016819 0.3821685 -1.047693
203 -1.016819 0.3821685 -1.047693
204 -1.016819 0.3821685 -1.047693
209 -1.016819 0.3821685 -1.047693
210 -1.016819 0.3821685 -1.047693
211 -1.016819 0.3821685 -1.047693
212 -1.016819 0.3821685 -1.047693
213 -1.016819 0.3821685 -1.047693
214 -1.016819 0.3821685 -1.047693
217 -1.016819 0.3821685 -1.047693
218 -1.016819 0.3821685 -1.047693
219 -1.016819 0.3821685 -1.047693
220 -1.016819 0.3821685 -1.047693
221 -1.016819 0.3821685 -1.047693
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 2.095037 0.8358312 0.9710525 1.109468
4 2.095037 0.8358312 0.9710525 1.109468
11 2.095037 0.8358312 0.9710525 1.109468
12 2.095037 0.8358312 0.9710525 1.109468
19 2.095037 0.8358312 0.9710525 1.109468
20 2.095037 0.8358312 0.9710525 1.109468
26 2.095037 0.8358312 0.9710525 1.109468
27 2.095037 0.8358312 0.9710525 1.109468
35 2.095037 0.8358312 0.9710525 1.109468
36 2.095037 0.8358312 0.9710525 1.109468
41 2.095037 0.8358312 0.9710525 1.109468
42 2.095037 0.8358312 0.9710525 1.109468
43 2.095037 0.8358312 0.9710525 1.109468
44 2.095037 0.8358312 0.9710525 1.109468
45 2.095037 0.8358312 0.9710525 1.109468
46 2.095037 0.8358312 0.9710525 1.109468
201 2.095037 0.8358312 0.9710525 1.109468
202 2.095037 0.8358312 0.9710525 1.109468
203 2.095037 0.8358312 0.9710525 1.109468
204 2.095037 0.8358312 0.9710525 1.109468
209 2.095037 0.8358312 0.9710525 1.109468
210 2.095037 0.8358312 0.9710525 1.109468
211 2.095037 0.8358312 0.9710525 1.109468
212 2.095037 0.8358312 0.9710525 1.109468
213 2.095037 0.8358312 0.9710525 1.109468
214 2.095037 0.8358312 0.9710525 1.109468
217 2.095037 0.8358312 0.9710525 1.109468
218 2.095037 0.8358312 0.9710525 1.109468
219 2.095037 0.8358312 0.9710525 1.109468
220 2.095037 0.8358312 0.9710525 1.109468
221 2.095037 0.8358312 0.9710525 1.109468
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
4 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
11 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
12 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
19 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
20 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
26 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
27 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
35 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
36 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
41 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
42 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
43 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
44 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
45 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
46 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
201 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
202 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
203 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
204 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
209 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
210 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
211 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
212 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
213 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
214 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
217 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
218 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
219 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
220 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
221 -2.515335 -0.139798 0.2827152 0.1251637 -0.307251
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 0.8854134 0.2021629 -0.9210301 -0.4863227
4 0.8854134 0.2021629 -0.9210301 -0.4863227
11 0.8854134 0.2021629 -0.9210301 -0.4863227
12 0.8854134 0.2021629 -0.9210301 -0.4863227
19 0.8854134 0.2021629 -0.9210301 -0.4863227
20 0.8854134 0.2021629 -0.9210301 -0.4863227
26 0.8854134 0.2021629 -0.9210301 -0.4863227
27 0.8854134 0.2021629 -0.9210301 -0.4863227
35 0.8854134 0.2021629 -0.9210301 -0.4863227
36 0.8854134 0.2021629 -0.9210301 -0.4863227
41 0.8854134 0.2021629 -0.9210301 -0.4863227
42 0.8854134 0.2021629 -0.9210301 -0.4863227
43 0.8854134 0.2021629 -0.9210301 -0.4863227
44 0.8854134 0.2021629 -0.9210301 -0.4863227
45 0.8854134 0.2021629 -0.9210301 -0.4863227
46 0.8854134 0.2021629 -0.9210301 -0.4863227
201 0.8854134 0.2021629 -0.9210301 -0.4863227
202 0.8854134 0.2021629 -0.9210301 -0.4863227
203 0.8854134 0.2021629 -0.9210301 -0.4863227
204 0.8854134 0.2021629 -0.9210301 -0.4863227
209 0.8854134 0.2021629 -0.9210301 -0.4863227
210 0.8854134 0.2021629 -0.9210301 -0.4863227
211 0.8854134 0.2021629 -0.9210301 -0.4863227
212 0.8854134 0.2021629 -0.9210301 -0.4863227
213 0.8854134 0.2021629 -0.9210301 -0.4863227
214 0.8854134 0.2021629 -0.9210301 -0.4863227
217 0.8854134 0.2021629 -0.9210301 -0.4863227
218 0.8854134 0.2021629 -0.9210301 -0.4863227
219 0.8854134 0.2021629 -0.9210301 -0.4863227
220 0.8854134 0.2021629 -0.9210301 -0.4863227
221 0.8854134 0.2021629 -0.9210301 -0.4863227
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 2.270789 2.686168
4 2.270789 2.686168
11 2.270789 2.686168
12 2.270789 2.686168
19 2.270789 2.686168
20 2.270789 2.686168
26 2.270789 2.686168
27 2.270789 2.686168
35 2.270789 2.686168
36 2.270789 2.686168
41 2.270789 2.686168
42 2.270789 2.686168
43 2.270789 2.686168
44 2.270789 2.686168
45 2.270789 2.686168
46 2.270789 2.686168
201 2.270789 2.686168
202 2.270789 2.686168
203 2.270789 2.686168
204 2.270789 2.686168
209 2.270789 2.686168
210 2.270789 2.686168
211 2.270789 2.686168
212 2.270789 2.686168
213 2.270789 2.686168
214 2.270789 2.686168
217 2.270789 2.686168
218 2.270789 2.686168
219 2.270789 2.686168
220 2.270789 2.686168
221 2.270789 2.686168
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 2.396537 0.1454746
4 2.396537 0.1454746
11 2.396537 0.1454746
12 2.396537 0.1454746
19 2.396537 0.1454746
20 2.396537 0.1454746
26 2.396537 0.1454746
27 2.396537 0.1454746
35 2.396537 0.1454746
36 2.396537 0.1454746
41 2.396537 0.1454746
42 2.396537 0.1454746
43 2.396537 0.1454746
44 2.396537 0.1454746
45 2.396537 0.1454746
46 2.396537 0.1454746
201 2.396537 0.1454746
202 2.396537 0.1454746
203 2.396537 0.1454746
204 2.396537 0.1454746
209 2.396537 0.1454746
210 2.396537 0.1454746
211 2.396537 0.1454746
212 2.396537 0.1454746
213 2.396537 0.1454746
214 2.396537 0.1454746
217 2.396537 0.1454746
218 2.396537 0.1454746
219 2.396537 0.1454746
220 2.396537 0.1454746
221 2.396537 0.1454746
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -1.325835 3.354634
4 -1.325835 3.354634
11 -1.325835 3.354634
12 -1.325835 3.354634
19 -1.325835 3.354634
20 -1.325835 3.354634
26 -1.325835 3.354634
27 -1.325835 3.354634
35 -1.325835 3.354634
36 -1.325835 3.354634
41 -1.325835 3.354634
42 -1.325835 3.354634
43 -1.325835 3.354634
44 -1.325835 3.354634
45 -1.325835 3.354634
46 -1.325835 3.354634
201 -1.325835 3.354634
202 -1.325835 3.354634
203 -1.325835 3.354634
204 -1.325835 3.354634
209 -1.325835 3.354634
210 -1.325835 3.354634
211 -1.325835 3.354634
212 -1.325835 3.354634
213 -1.325835 3.354634
214 -1.325835 3.354634
217 -1.325835 3.354634
218 -1.325835 3.354634
219 -1.325835 3.354634
220 -1.325835 3.354634
221 -1.325835 3.354634
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
AFDWfig<-ggplot(phys, aes(y=AFDW_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Total~biomass~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
AFDWfig
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
AFDW_stress_fig<-ggplot(phys_stress, aes(y=AFDW_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=AFDW_mg.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=AFDW_mg.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
#geom_point(size=1.5, position= pd)+
#geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Total~biomass~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
AFDW_stress_fig
library(Rmisc)
AFDW_sum<-summarySE(phys, measurevar='AFDW_mg.cm.2', groupvars=c('Date'), na.rm=TRUE, conf.interval = 0.95)
AFDW_sumAFDWfig_3<-ggplot(AFDW_sum, aes(y=AFDW_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=AFDW_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=AFDW_mg.cm.2-se, ymax=AFDW_mg.cm.2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(AFDW~(mg~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statAFDWfig_3
##Lipids ###Normality
hist(phys$Lipid..g.per.cm2.)
lipid.lm<- lm(Lipid..g.per.cm2.~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(lipid.lm, ask=FALSE, which=1:6)
###Stats
lipid.lme <- lme(Lipid..g.per.cm2.~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(lipid.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, SpeciesPorites compressa:Months10, BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months10Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Lipid..g.per.cm2.
Chisq Df Pr(>Chisq)
(Intercept) 42.9681 1 5.564e-11 ***
Species 1.1903 1 0.2752703
Bleach 0.4293 1 0.5123488
Months 26.2142 6 0.0002031 ***
Species:Bleach 0.2500 1 0.6170538
Species:Months 25.1997 6 0.0003136 ***
Bleach:Months 5.1717 6 0.5219914
Species:Bleach:Months 14.8464 6 0.0214855 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(lipid.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 10 8.75 0.954 41 6.82 10.68
Porites compressa 10 10.23 0.899 40 8.41 12.05
Montipora capitata 12 3.24 0.848 41 1.53 4.95
Porites compressa 12 5.50 0.894 40 3.69 7.30
Montipora capitata 17 6.61 0.871 41 4.86 8.37
Porites compressa 17 11.13 0.934 40 9.24 13.02
Montipora capitata 20 7.19 0.871 41 5.44 8.95
Porites compressa 20 12.60 0.894 40 10.79 14.40
Montipora capitata 24 4.37 0.920 41 2.51 6.23
Porites compressa 24 7.08 1.052 40 4.96 9.21
Montipora capitata 29 7.58 0.893 41 5.78 9.39
Porites compressa 29 9.31 0.947 40 7.39 11.22
Montipora capitata 35 11.22 1.183 41 8.84 13.61
Porites compressa 35 7.11 1.266 40 4.55 9.66
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months10 - Months12 5.5106 1.24 161 4.458 0.0003
Months10 - Months17 2.1337 1.25 161 1.707 0.6125
Months10 - Months20 1.5547 1.25 161 1.241 0.8769
Months10 - Months24 4.3770 1.28 161 3.417 0.0139
Months10 - Months29 1.1643 1.26 161 0.921 0.9687
Months10 - Months35 -2.4760 1.49 161 -1.660 0.6437
Months12 - Months17 -3.3768 1.17 161 -2.878 0.0668
Months12 - Months20 -3.9558 1.17 161 -3.372 0.0160
Months12 - Months24 -1.1335 1.21 161 -0.937 0.9660
Months12 - Months29 -4.3463 1.19 161 -3.653 0.0063
Months12 - Months35 -7.9866 1.43 161 -5.596 <.0001
Months17 - Months20 -0.5790 1.19 161 -0.487 0.9990
Months17 - Months24 2.2433 1.22 161 1.832 0.5287
Months17 - Months29 -0.9694 1.20 161 -0.805 0.9842
Months17 - Months35 -4.6098 1.44 161 -3.202 0.0269
Months20 - Months24 2.8223 1.23 161 2.300 0.2503
Months20 - Months29 -0.3905 1.21 161 -0.324 0.9999
Months20 - Months35 -4.0308 1.44 161 -2.799 0.0820
Months24 - Months29 -3.2127 1.24 161 -2.594 0.1349
Months24 - Months35 -6.8531 1.47 161 -4.657 0.0001
Months29 - Months35 -3.6403 1.45 161 -2.507 0.1637
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months10 - Months12 4.7338 1.22 161 3.871 0.0029
Months10 - Months17 -0.8993 1.25 161 -0.718 0.9913
Months10 - Months20 -2.3651 1.22 161 -1.934 0.4610
Months10 - Months24 3.1486 1.34 161 2.345 0.2296
Months10 - Months29 0.9243 1.26 161 0.732 0.9904
Months10 - Months35 3.1257 1.52 161 2.052 0.3867
Months12 - Months17 -5.6331 1.25 161 -4.512 0.0002
Months12 - Months20 -7.0990 1.22 161 -5.825 <.0001
Months12 - Months24 -1.5852 1.34 161 -1.184 0.8994
Months12 - Months29 -3.8096 1.26 161 -3.027 0.0446
Months12 - Months35 -1.6082 1.52 161 -1.058 0.9392
Months17 - Months20 -1.4659 1.25 161 -1.174 0.9029
Months17 - Months24 4.0479 1.37 161 2.960 0.0536
Months17 - Months29 1.8236 1.29 161 1.416 0.7924
Months17 - Months35 4.0250 1.54 161 2.609 0.1302
Months20 - Months24 5.5138 1.34 161 4.117 0.0012
Months20 - Months29 3.2894 1.26 161 2.614 0.1287
Months20 - Months35 5.4908 1.52 161 3.613 0.0073
Months24 - Months29 -2.2243 1.37 161 -1.622 0.6684
Months24 - Months35 -0.0229 1.62 161 -0.014 1.0000
Months29 - Months35 2.2014 1.55 161 1.421 0.7897
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 7 estimates summary(lipid.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 1.010679 3.656391
Fixed effects: Lipid..g.per.cm2. ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M12 SPc:M17
SpeciesPorites compressa -0.730
BleachNon-bleach -0.749 0.547
Months12 -0.750 0.548 0.562
Months17 -0.731 0.534 0.548 0.577
Months20 -0.734 0.536 0.550 0.579 0.564
Months24 -0.709 0.518 0.532 0.560 0.549 0.547
Months29 -0.731 0.534 0.548 0.577 0.566 0.564 0.549
Months35 -0.590 0.431 0.442 0.460 0.450 0.451 0.433 0.450
SpeciesPorites compressa:BleachNon-bleach 0.546 -0.747 -0.729 -0.410 -0.399 -0.401 -0.387 -0.399 -0.322
SpeciesPorites compressa:Months12 0.535 -0.729 -0.401 -0.713 -0.412 -0.413 -0.399 -0.412 -0.328 0.547
SpeciesPorites compressa:Months17 0.511 -0.695 -0.383 -0.403 -0.698 -0.394 -0.383 -0.395 -0.314 0.520 0.536
SpeciesPorites compressa:Months20 0.530 -0.721 -0.397 -0.418 -0.407 -0.722 -0.395 -0.407 -0.326 0.540 0.556 0.530
SpeciesPorites compressa:Months24 0.500 -0.687 -0.374 -0.395 -0.386 -0.385 -0.704 -0.386 -0.305 0.518 0.528 0.506
SpeciesPorites compressa:Months29 0.518 -0.710 -0.388 -0.409 -0.401 -0.400 -0.389 -0.709 -0.319 0.534 0.546 0.523
SpeciesPorites compressa:Months35 0.437 -0.597 -0.327 -0.341 -0.333 -0.334 -0.320 -0.333 -0.740 0.446 0.452 0.434
BleachNon-bleach:Months12 0.550 -0.401 -0.729 -0.733 -0.423 -0.424 -0.410 -0.423 -0.337 0.531 0.523 0.295
BleachNon-bleach:Months17 0.541 -0.395 -0.719 -0.427 -0.740 -0.417 -0.406 -0.418 -0.333 0.524 0.305 0.516
BleachNon-bleach:Months20 0.544 -0.397 -0.720 -0.429 -0.418 -0.741 -0.405 -0.418 -0.334 0.525 0.306 0.292
BleachNon-bleach:Months24 0.525 -0.383 -0.697 -0.414 -0.406 -0.405 -0.740 -0.406 -0.320 0.508 0.296 0.283
BleachNon-bleach:Months29 0.535 -0.391 -0.709 -0.422 -0.414 -0.413 -0.401 -0.731 -0.329 0.517 0.301 0.289
BleachNon-bleach:Months35 0.462 -0.337 -0.610 -0.360 -0.352 -0.353 -0.339 -0.352 -0.783 0.444 0.257 0.246
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.390 0.531 0.517 0.520 0.300 0.301 0.291 0.300 0.239 -0.709 -0.730 -0.391
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.382 0.520 0.508 0.302 0.523 0.295 0.287 0.296 0.235 -0.694 -0.401 -0.748
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.388 0.528 0.515 0.307 0.299 0.529 0.290 0.299 0.239 -0.704 -0.409 -0.389
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.360 0.498 0.479 0.285 0.279 0.278 0.508 0.279 0.220 -0.665 -0.382 -0.366
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.377 0.518 0.499 0.297 0.291 0.291 0.283 0.515 0.232 -0.691 -0.398 -0.382
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.323 0.441 0.427 0.252 0.246 0.247 0.237 0.246 0.548 -0.584 -0.335 -0.321
SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M12 BN-:M17 BN-:M20 BN-:M24 BN-:M29 BN-:M3 SPc:BN-:M12
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24 0.522
SpeciesPorites compressa:Months29 0.540 0.519
SpeciesPorites compressa:Months35 0.448 0.424 0.442
BleachNon-bleach:Months12 0.306 0.289 0.300 0.249
BleachNon-bleach:Months17 0.301 0.286 0.296 0.246 0.555
BleachNon-bleach:Months20 0.535 0.285 0.296 0.247 0.556 0.548
BleachNon-bleach:Months24 0.292 0.521 0.288 0.237 0.538 0.532 0.531
BleachNon-bleach:Months29 0.298 0.283 0.518 0.244 0.547 0.541 0.540 0.526
BleachNon-bleach:Months35 0.255 0.239 0.250 0.580 0.465 0.460 0.461 0.445 0.455
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.406 -0.386 -0.399 -0.330 -0.710 -0.394 -0.395 -0.382 -0.388 -0.330
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.397 -0.378 -0.392 -0.325 -0.392 -0.707 -0.387 -0.376 -0.382 -0.325 0.522
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.734 -0.384 -0.397 -0.328 -0.397 -0.391 -0.715 -0.380 -0.386 -0.329 0.531
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.377 -0.725 -0.378 -0.307 -0.369 -0.365 -0.365 -0.687 -0.361 -0.306 0.497
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.393 -0.381 -0.730 -0.322 -0.385 -0.381 -0.380 -0.371 -0.704 -0.320 0.517
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.332 -0.313 -0.327 -0.740 -0.326 -0.322 -0.322 -0.311 -0.318 -0.700 0.435
SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months12
SpeciesPorites compressa:BleachNon-bleach:Months17
SpeciesPorites compressa:BleachNon-bleach:Months20 0.519
SpeciesPorites compressa:BleachNon-bleach:Months24 0.488 0.494
SpeciesPorites compressa:BleachNon-bleach:Months29 0.508 0.514 0.491
SpeciesPorites compressa:BleachNon-bleach:Months35 0.427 0.433 0.404 0.423
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.5495646 -0.5922700 -0.1244094 0.3912743 4.4912839
Number of Observations: 229
Number of Groups: 42 r.squaredGLMM(lipid.lme) R2m R2c
[1,] 0.3634548 0.4086378####Coefficients
coef(lipid.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months12 Months17 Months20 Months24 Months29 Months35
3 9.942599 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
4 9.788180 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
11 9.053353 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
12 9.419682 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
19 9.741812 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
20 9.025127 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
26 9.200463 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
27 9.190986 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
41 10.418310 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
42 10.624788 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
43 9.521996 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
44 8.367029 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
45 9.229039 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
46 8.800990 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
201 9.038190 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
202 9.781263 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
203 9.008659 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
204 9.265856 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
209 10.246873 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
210 9.237636 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
211 8.700658 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
212 9.756056 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
213 9.244713 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
214 10.087347 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
217 9.552819 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
218 9.450237 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
219 9.553414 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
220 8.842221 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
221 9.028359 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
222 8.457844 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
225 9.462530 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
229 9.332277 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
230 9.005645 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
235 9.588284 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
237 9.373910 2.136835 -1.250194 -6.310396 -3.705425 -1.970119 -4.561315 -2.964185 3.170416
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months12 SpeciesPorites compressa:Months17
3 -1.309363 -0.9177666 3.575922
4 -1.309363 -0.9177666 3.575922
11 -1.309363 -0.9177666 3.575922
12 -1.309363 -0.9177666 3.575922
19 -1.309363 -0.9177666 3.575922
20 -1.309363 -0.9177666 3.575922
26 -1.309363 -0.9177666 3.575922
27 -1.309363 -0.9177666 3.575922
41 -1.309363 -0.9177666 3.575922
42 -1.309363 -0.9177666 3.575922
43 -1.309363 -0.9177666 3.575922
44 -1.309363 -0.9177666 3.575922
45 -1.309363 -0.9177666 3.575922
46 -1.309363 -0.9177666 3.575922
201 -1.309363 -0.9177666 3.575922
202 -1.309363 -0.9177666 3.575922
203 -1.309363 -0.9177666 3.575922
204 -1.309363 -0.9177666 3.575922
209 -1.309363 -0.9177666 3.575922
210 -1.309363 -0.9177666 3.575922
211 -1.309363 -0.9177666 3.575922
212 -1.309363 -0.9177666 3.575922
213 -1.309363 -0.9177666 3.575922
214 -1.309363 -0.9177666 3.575922
217 -1.309363 -0.9177666 3.575922
218 -1.309363 -0.9177666 3.575922
219 -1.309363 -0.9177666 3.575922
220 -1.309363 -0.9177666 3.575922
221 -1.309363 -0.9177666 3.575922
222 -1.309363 -0.9177666 3.575922
225 -1.309363 -0.9177666 3.575922
229 -1.309363 -0.9177666 3.575922
230 -1.309363 -0.9177666 3.575922
235 -1.309363 -0.9177666 3.575922
237 -1.309363 -0.9177666 3.575922
SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35
3 2.932109 -0.4916699 3.068148 -9.934488
4 2.932109 -0.4916699 3.068148 -9.934488
11 2.932109 -0.4916699 3.068148 -9.934488
12 2.932109 -0.4916699 3.068148 -9.934488
19 2.932109 -0.4916699 3.068148 -9.934488
20 2.932109 -0.4916699 3.068148 -9.934488
26 2.932109 -0.4916699 3.068148 -9.934488
27 2.932109 -0.4916699 3.068148 -9.934488
41 2.932109 -0.4916699 3.068148 -9.934488
42 2.932109 -0.4916699 3.068148 -9.934488
43 2.932109 -0.4916699 3.068148 -9.934488
44 2.932109 -0.4916699 3.068148 -9.934488
45 2.932109 -0.4916699 3.068148 -9.934488
46 2.932109 -0.4916699 3.068148 -9.934488
201 2.932109 -0.4916699 3.068148 -9.934488
202 2.932109 -0.4916699 3.068148 -9.934488
203 2.932109 -0.4916699 3.068148 -9.934488
204 2.932109 -0.4916699 3.068148 -9.934488
209 2.932109 -0.4916699 3.068148 -9.934488
210 2.932109 -0.4916699 3.068148 -9.934488
211 2.932109 -0.4916699 3.068148 -9.934488
212 2.932109 -0.4916699 3.068148 -9.934488
213 2.932109 -0.4916699 3.068148 -9.934488
214 2.932109 -0.4916699 3.068148 -9.934488
217 2.932109 -0.4916699 3.068148 -9.934488
218 2.932109 -0.4916699 3.068148 -9.934488
219 2.932109 -0.4916699 3.068148 -9.934488
220 2.932109 -0.4916699 3.068148 -9.934488
221 2.932109 -0.4916699 3.068148 -9.934488
222 2.932109 -0.4916699 3.068148 -9.934488
225 2.932109 -0.4916699 3.068148 -9.934488
229 2.932109 -0.4916699 3.068148 -9.934488
230 2.932109 -0.4916699 3.068148 -9.934488
235 2.932109 -0.4916699 3.068148 -9.934488
237 2.932109 -0.4916699 3.068148 -9.934488
BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20 BleachNon-bleach:Months24 BleachNon-bleach:Months29
3 1.599679 3.143435 0.8308004 0.3686042 3.599838
4 1.599679 3.143435 0.8308004 0.3686042 3.599838
11 1.599679 3.143435 0.8308004 0.3686042 3.599838
12 1.599679 3.143435 0.8308004 0.3686042 3.599838
19 1.599679 3.143435 0.8308004 0.3686042 3.599838
20 1.599679 3.143435 0.8308004 0.3686042 3.599838
26 1.599679 3.143435 0.8308004 0.3686042 3.599838
27 1.599679 3.143435 0.8308004 0.3686042 3.599838
41 1.599679 3.143435 0.8308004 0.3686042 3.599838
42 1.599679 3.143435 0.8308004 0.3686042 3.599838
43 1.599679 3.143435 0.8308004 0.3686042 3.599838
44 1.599679 3.143435 0.8308004 0.3686042 3.599838
45 1.599679 3.143435 0.8308004 0.3686042 3.599838
46 1.599679 3.143435 0.8308004 0.3686042 3.599838
201 1.599679 3.143435 0.8308004 0.3686042 3.599838
202 1.599679 3.143435 0.8308004 0.3686042 3.599838
203 1.599679 3.143435 0.8308004 0.3686042 3.599838
204 1.599679 3.143435 0.8308004 0.3686042 3.599838
209 1.599679 3.143435 0.8308004 0.3686042 3.599838
210 1.599679 3.143435 0.8308004 0.3686042 3.599838
211 1.599679 3.143435 0.8308004 0.3686042 3.599838
212 1.599679 3.143435 0.8308004 0.3686042 3.599838
213 1.599679 3.143435 0.8308004 0.3686042 3.599838
214 1.599679 3.143435 0.8308004 0.3686042 3.599838
217 1.599679 3.143435 0.8308004 0.3686042 3.599838
218 1.599679 3.143435 0.8308004 0.3686042 3.599838
219 1.599679 3.143435 0.8308004 0.3686042 3.599838
220 1.599679 3.143435 0.8308004 0.3686042 3.599838
221 1.599679 3.143435 0.8308004 0.3686042 3.599838
222 1.599679 3.143435 0.8308004 0.3686042 3.599838
225 1.599679 3.143435 0.8308004 0.3686042 3.599838
229 1.599679 3.143435 0.8308004 0.3686042 3.599838
230 1.599679 3.143435 0.8308004 0.3686042 3.599838
235 1.599679 3.143435 0.8308004 0.3686042 3.599838
237 1.599679 3.143435 0.8308004 0.3686042 3.599838
BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 -1.388747 3.388956 -1.085877
4 -1.388747 3.388956 -1.085877
11 -1.388747 3.388956 -1.085877
12 -1.388747 3.388956 -1.085877
19 -1.388747 3.388956 -1.085877
20 -1.388747 3.388956 -1.085877
26 -1.388747 3.388956 -1.085877
27 -1.388747 3.388956 -1.085877
41 -1.388747 3.388956 -1.085877
42 -1.388747 3.388956 -1.085877
43 -1.388747 3.388956 -1.085877
44 -1.388747 3.388956 -1.085877
45 -1.388747 3.388956 -1.085877
46 -1.388747 3.388956 -1.085877
201 -1.388747 3.388956 -1.085877
202 -1.388747 3.388956 -1.085877
203 -1.388747 3.388956 -1.085877
204 -1.388747 3.388956 -1.085877
209 -1.388747 3.388956 -1.085877
210 -1.388747 3.388956 -1.085877
211 -1.388747 3.388956 -1.085877
212 -1.388747 3.388956 -1.085877
213 -1.388747 3.388956 -1.085877
214 -1.388747 3.388956 -1.085877
217 -1.388747 3.388956 -1.085877
218 -1.388747 3.388956 -1.085877
219 -1.388747 3.388956 -1.085877
220 -1.388747 3.388956 -1.085877
221 -1.388747 3.388956 -1.085877
222 -1.388747 3.388956 -1.085877
225 -1.388747 3.388956 -1.085877
229 -1.388747 3.388956 -1.085877
230 -1.388747 3.388956 -1.085877
235 -1.388747 3.388956 -1.085877
237 -1.388747 3.388956 -1.085877
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 1.975481 3.440108
4 1.975481 3.440108
11 1.975481 3.440108
12 1.975481 3.440108
19 1.975481 3.440108
20 1.975481 3.440108
26 1.975481 3.440108
27 1.975481 3.440108
41 1.975481 3.440108
42 1.975481 3.440108
43 1.975481 3.440108
44 1.975481 3.440108
45 1.975481 3.440108
46 1.975481 3.440108
201 1.975481 3.440108
202 1.975481 3.440108
203 1.975481 3.440108
204 1.975481 3.440108
209 1.975481 3.440108
210 1.975481 3.440108
211 1.975481 3.440108
212 1.975481 3.440108
213 1.975481 3.440108
214 1.975481 3.440108
217 1.975481 3.440108
218 1.975481 3.440108
219 1.975481 3.440108
220 1.975481 3.440108
221 1.975481 3.440108
222 1.975481 3.440108
225 1.975481 3.440108
229 1.975481 3.440108
230 1.975481 3.440108
235 1.975481 3.440108
237 1.975481 3.440108
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -5.656341 8.66553
4 -5.656341 8.66553
11 -5.656341 8.66553
12 -5.656341 8.66553
19 -5.656341 8.66553
20 -5.656341 8.66553
26 -5.656341 8.66553
27 -5.656341 8.66553
41 -5.656341 8.66553
42 -5.656341 8.66553
43 -5.656341 8.66553
44 -5.656341 8.66553
45 -5.656341 8.66553
46 -5.656341 8.66553
201 -5.656341 8.66553
202 -5.656341 8.66553
203 -5.656341 8.66553
204 -5.656341 8.66553
209 -5.656341 8.66553
210 -5.656341 8.66553
211 -5.656341 8.66553
212 -5.656341 8.66553
213 -5.656341 8.66553
214 -5.656341 8.66553
217 -5.656341 8.66553
218 -5.656341 8.66553
219 -5.656341 8.66553
220 -5.656341 8.66553
221 -5.656341 8.66553
222 -5.656341 8.66553
225 -5.656341 8.66553
229 -5.656341 8.66553
230 -5.656341 8.66553
235 -5.656341 8.66553
237 -5.656341 8.66553
[ reached 'max' / getOption("max.print") -- omitted 7 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
lipidfig<-ggplot(phys, aes(y=Lipid..g.per.cm2., x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Lipids~(g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
lipidfig
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
lipid_stress_fig<-ggplot(phys_stress, aes(y=Lipid..g.per.cm2., x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Lipid..g.per.cm2., x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Lipid..g.per.cm2., x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
#geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
#geom_point(size=1.5, position= pd)+
#geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Lipids~(g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
lipid_stress_fig
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
lipid_stress_fig<-ggplot(phys_stress, aes(y=Lipid..g.per.cm2., x=Months, color=Bleach, fill=Bleach))+
geom_boxplot(alpha=0.6, color= "black")+
#geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
#geom_point(size=1.5, position= pd)+
#geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Lipids~(g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
lipid_stress_fig
lipidfig_3<-ggplot(lipid_sum, aes(y=Lipid..g.per.cm2., x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=lipid_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Lipid..g.per.cm2.-se, ymax=Lipid..g.per.cm2.+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Lipid~(g~'\U2219'~cm^{-2})), limits=c(0,15),breaks=c(0,5,10,15))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statlipidfig_3
##TAC ###Normality
hist(phys$TAC_CRE.mgprotein.1)
tac.lm<- lm(TAC_CRE.mgprotein.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(tac.lm, ask=FALSE, which=1:6)
###Stats
tac.lme <- lme(TAC_CRE.mgprotein.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(tac.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months35, SpeciesPorites compressa:Months35, BleachNon-bleach:Months35, SpeciesPorites compressa:BleachNon-bleach:Months35Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: TAC_CRE.mgprotein.1
Chisq Df Pr(>Chisq)
(Intercept) 0.0103 1 0.9190
Species 0.0972 1 0.7553
Bleach 0.0013 1 0.9716
Months 29.7361 6 4.412e-05 ***
Species:Bleach 0.0010 1 0.9749
Species:Months 10.3506 6 0.1106
Bleach:Months 2.2436 6 0.8960
Species:Bleach:Months 1.8121 6 0.9361
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(tac.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 2193 12221 39 -22525 26911
Porites compressa 0 9267 12221 38 -15472 34007
Montipora capitata 10 11748 13770 39 -16105 39602
Porites compressa 10 37340 12962 38 11100 63580
Montipora capitata 12 10633 12221 39 -14086 35351
Porites compressa 12 62047 12882 38 35970 88124
Montipora capitata 17 61775 12221 39 37057 86494
Porites compressa 17 45547 12962 38 19307 71787
Montipora capitata 20 26684 12555 39 1288 52079
Porites compressa 20 45007 12882 38 18930 71085
Montipora capitata 24 89055 12881 39 63000 115110
Porites compressa 24 67205 14606 38 37637 96772
Montipora capitata 29 7380 12881 39 -18675 33435
Porites compressa 29 31989 13663 38 4330 59647
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months0 - Months10 -9555 18340 187 -0.521 0.9985
Months0 - Months12 -8440 17207 187 -0.491 0.9990
Months0 - Months17 -59582 17207 187 -3.463 0.0116
Months0 - Months20 -24491 17446 187 -1.404 0.7993
Months0 - Months24 -86862 17682 187 -4.912 <.0001
Months0 - Months29 -5187 17682 187 -0.293 0.9999
Months10 - Months12 1115 18340 187 0.061 1.0000
Months10 - Months17 -50027 18340 187 -2.728 0.0971
Months10 - Months20 -14935 18566 187 -0.804 0.9843
Months10 - Months24 -77307 18779 187 -4.117 0.0011
Months10 - Months29 4368 18779 187 0.233 1.0000
Months12 - Months17 -51142 17207 187 -2.972 0.0512
Months12 - Months20 -16051 17446 187 -0.920 0.9690
Months12 - Months24 -78422 17682 187 -4.435 0.0003
Months12 - Months29 3253 17682 187 0.184 1.0000
Months17 - Months20 35092 17446 187 2.011 0.4110
Months17 - Months24 -27280 17682 187 -1.543 0.7186
Months17 - Months29 54396 17682 187 3.076 0.0382
Months20 - Months24 -62372 17916 187 -3.481 0.0109
Months20 - Months29 19304 17916 187 1.077 0.9340
Months24 - Months29 81676 18138 187 4.503 0.0002
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months0 - Months10 -28073 17741 187 -1.582 0.6938
Months0 - Months12 -52780 17682 187 -2.985 0.0494
Months0 - Months17 -36280 17741 187 -2.045 0.3901
Months0 - Months20 -35740 17682 187 -2.021 0.4048
Months0 - Months24 -57937 18975 187 -3.053 0.0408
Months0 - Months29 -22722 18259 187 -1.244 0.8757
Months10 - Months12 -24707 18195 187 -1.358 0.8232
Months10 - Months17 -8207 18251 187 -0.450 0.9994
Months10 - Months20 -7668 18195 187 -0.421 0.9996
Months10 - Months24 -29865 19454 187 -1.535 0.7233
Months10 - Months29 5351 18756 187 0.285 1.0000
Months12 - Months17 16500 18195 187 0.907 0.9711
Months12 - Months20 17039 18138 187 0.939 0.9656
Months12 - Months24 -5158 19400 187 -0.266 1.0000
Months12 - Months29 30058 18700 187 1.607 0.6778
Months17 - Months20 539 18195 187 0.030 1.0000
Months17 - Months24 -21658 19454 187 -1.113 0.9234
Months17 - Months29 13558 18756 187 0.723 0.9911
Months20 - Months24 -22197 19400 187 -1.144 0.9135
Months20 - Months29 13019 18700 187 0.696 0.9927
Months24 - Months29 35216 19919 187 1.768 0.5713
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 7 estimates summary(tac.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 5110.805 54412.56
Fixed effects: TAC_CRE.mgprotein.1 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 SpPc:BN- SPc:M10 SPc:M12
SpeciesPorites compressa -0.707
BleachNon-bleach -0.707 0.500
Months10 -0.638 0.451 0.451
Months12 -0.704 0.498 0.498 0.453
Months17 -0.704 0.498 0.498 0.453 0.500
Months20 -0.685 0.484 0.484 0.441 0.487 0.487
Months24 -0.685 0.484 0.484 0.442 0.487 0.487 0.473
Months29 -0.685 0.484 0.484 0.442 0.487 0.487 0.473 0.474
SpeciesPorites compressa:BleachNon-bleach 0.500 -0.707 -0.707 -0.319 -0.352 -0.352 -0.343 -0.343 -0.343
SpeciesPorites compressa:Months10 0.460 -0.651 -0.325 -0.721 -0.327 -0.327 -0.318 -0.318 -0.318 0.460
SpeciesPorites compressa:Months12 0.491 -0.694 -0.347 -0.316 -0.697 -0.349 -0.339 -0.339 -0.339 0.491 0.456
SpeciesPorites compressa:Months17 0.483 -0.683 -0.341 -0.311 -0.343 -0.686 -0.334 -0.334 -0.334 0.483 0.449 0.479
SpeciesPorites compressa:Months20 0.484 -0.685 -0.343 -0.312 -0.344 -0.344 -0.707 -0.335 -0.335 0.484 0.450 0.480
SpeciesPorites compressa:Months24 0.467 -0.661 -0.330 -0.301 -0.332 -0.332 -0.323 -0.682 -0.323 0.468 0.434 0.463
SpeciesPorites compressa:Months29 0.476 -0.674 -0.337 -0.307 -0.338 -0.338 -0.329 -0.330 -0.695 0.477 0.443 0.472
BleachNon-bleach:Months10 0.467 -0.330 -0.661 -0.732 -0.332 -0.332 -0.323 -0.323 -0.323 0.467 0.527 0.231
BleachNon-bleach:Months12 0.498 -0.352 -0.704 -0.321 -0.707 -0.354 -0.344 -0.344 -0.344 0.498 0.231 0.493
BleachNon-bleach:Months17 0.498 -0.352 -0.704 -0.321 -0.354 -0.707 -0.344 -0.344 -0.344 0.498 0.231 0.247
BleachNon-bleach:Months20 0.491 -0.347 -0.694 -0.316 -0.349 -0.349 -0.717 -0.339 -0.339 0.491 0.228 0.243
BleachNon-bleach:Months24 0.484 -0.343 -0.685 -0.312 -0.344 -0.344 -0.335 -0.707 -0.335 0.484 0.225 0.240
BleachNon-bleach:Months29 0.484 -0.343 -0.685 -0.312 -0.344 -0.344 -0.335 -0.335 -0.707 0.484 0.225 0.240
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.336 0.475 0.475 0.526 0.238 0.238 0.232 0.232 0.232 -0.672 -0.730 -0.333
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.347 0.491 0.491 0.224 0.493 0.247 0.240 0.240 0.240 -0.694 -0.322 -0.707
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.347 0.490 0.490 0.223 0.246 0.492 0.239 0.239 0.239 -0.693 -0.322 -0.343
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.345 0.488 0.488 0.222 0.245 0.245 0.503 0.238 0.238 -0.690 -0.320 -0.342
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.330 0.467 0.467 0.213 0.234 0.234 0.228 0.482 0.228 -0.661 -0.307 -0.327
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.337 0.477 0.476 0.217 0.239 0.239 0.233 0.233 0.492 -0.674 -0.313 -0.334
SPc:M17 SPc:M20 SPc:M24 SPc:M29 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24 BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20 0.472
SpeciesPorites compressa:Months24 0.455 0.457
SpeciesPorites compressa:Months29 0.464 0.466 0.450
BleachNon-bleach:Months10 0.227 0.228 0.220 0.225
BleachNon-bleach:Months12 0.242 0.243 0.234 0.239 0.469
BleachNon-bleach:Months17 0.485 0.243 0.234 0.239 0.469 0.500
BleachNon-bleach:Months20 0.239 0.507 0.231 0.236 0.463 0.493 0.493
BleachNon-bleach:Months24 0.236 0.237 0.482 0.233 0.457 0.487 0.487 0.480
BleachNon-bleach:Months29 0.236 0.237 0.228 0.492 0.457 0.487 0.487 0.480 0.474
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.327 -0.328 -0.316 -0.323 -0.719 -0.337 -0.337 -0.332 -0.328 -0.328
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.338 -0.339 -0.327 -0.334 -0.327 -0.697 -0.349 -0.344 -0.339 -0.339
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.718 -0.339 -0.326 -0.333 -0.327 -0.348 -0.696 -0.343 -0.339 -0.339
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.336 -0.712 -0.325 -0.332 -0.325 -0.346 -0.346 -0.702 -0.337 -0.337
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 -0.323 -0.707 -0.319 -0.311 -0.332 -0.332 -0.327 -0.681 -0.323
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.328 -0.329 -0.319 -0.707 -0.318 -0.338 -0.338 -0.334 -0.330 -0.695
SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
SpeciesPorites compressa:BleachNon-bleach:Months10
SpeciesPorites compressa:BleachNon-bleach:Months12 0.470
SpeciesPorites compressa:BleachNon-bleach:Months17 0.470 0.486
SpeciesPorites compressa:BleachNon-bleach:Months20 0.467 0.483 0.482
SpeciesPorites compressa:BleachNon-bleach:Months24 0.447 0.463 0.462 0.459
SpeciesPorites compressa:BleachNon-bleach:Months29 0.457 0.472 0.471 0.469 0.450
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-1.70732091 -0.27289636 -0.01668892 0.05405441 7.68396464
Number of Observations: 253
Number of Groups: 40 r.squaredGLMM(tac.lme) R2m R2c
[1,] 0.1924667 0.1995287####Coefficients
coef(tac.lme)tacsum<-summarySE(phys, measurevar = "TAC_CRE.mgprotein.1", groupvars = c("Species", "Months", "Bleach"), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedtacsum###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
tacfig<-ggplot(phys, aes(y=TAC_CRE.mgprotein.1, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
tacfig
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
tac_stress_fig<-ggplot(phys_stress, aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
#geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
#geom_point(size=1.5, position= pd)+
#geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
tac_stress_fig
library(Rmisc)
tac_sum<-summarySE(phys, measurevar='TAC_CRE.mgprotein.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedtac_sumtacfig_3<-ggplot(tac_sum, aes(y=TAC_CRE.mgprotein.1, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=tac_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=TAC_CRE.mgprotein.1-se, ymax=TAC_CRE.mgprotein.1+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: stattacfig_3
##Citrate synthase ###Normality
hist(phys$Citrate.synthase.mU.mg.protein.1)
cs.lm<- lm(Citrate.synthase.mU.mg.protein.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(cs.lm, ask=FALSE, which=1:6)
###Stats
cs.lme <- lme(Citrate.synthase.mU.mg.protein.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(cs.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, SpeciesPorites compressa:Months10, BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months10Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Citrate.synthase.mU.mg.protein.1
Chisq Df Pr(>Chisq)
(Intercept) 63.7819 1 1.390e-15 ***
Species 11.3170 1 0.000768 ***
Bleach 4.4265 1 0.035384 *
Months 32.7758 6 1.158e-05 ***
Species:Bleach 2.5453 1 0.110623
Species:Months 17.7884 6 0.006783 **
Bleach:Months 11.9362 6 0.063407 .
Species:Bleach:Months 5.9425 6 0.429658
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(cs.lme, list(pairwise ~ Bleach), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Bleach`
Bleach emmean SE df lower.CL upper.CL
Bleach 594 41.0 40 511 677
Non-bleach 660 40.6 40 577 742
Results are averaged over the levels of: Species, Months
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Bleach`
1 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -65.4 56.1 168 -1.166 0.2452
Results are averaged over the levels of: Species, Months
Degrees-of-freedom method: containment summary(cs.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 147.5101 270.986
Fixed effects: Citrate.synthase.mU.mg.protein.1 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M12 SPc:M17
SpeciesPorites compressa -0.730
BleachNon-bleach -0.745 0.544
Months12 -0.707 0.516 0.527
Months17 -0.707 0.516 0.527 0.597
Months20 -0.691 0.504 0.515 0.584 0.584
Months24 -0.686 0.500 0.511 0.579 0.579 0.566
Months29 -0.686 0.500 0.511 0.579 0.579 0.566 0.569
Months35 -0.559 0.408 0.417 0.453 0.453 0.446 0.444 0.444
SpeciesPorites compressa:BleachNon-bleach 0.547 -0.740 -0.734 -0.386 -0.386 -0.378 -0.375 -0.375 -0.306
SpeciesPorites compressa:Months12 0.505 -0.684 -0.376 -0.715 -0.427 -0.417 -0.414 -0.414 -0.324 0.516
SpeciesPorites compressa:Months17 0.499 -0.671 -0.372 -0.422 -0.706 -0.412 -0.409 -0.409 -0.320 0.503 0.555
SpeciesPorites compressa:Months20 0.500 -0.677 -0.373 -0.423 -0.423 -0.724 -0.410 -0.410 -0.323 0.510 0.559 0.549
SpeciesPorites compressa:Months24 0.475 -0.657 -0.354 -0.401 -0.401 -0.392 -0.693 -0.394 -0.308 0.501 0.537 0.525
SpeciesPorites compressa:Months29 0.485 -0.668 -0.361 -0.410 -0.410 -0.400 -0.402 -0.707 -0.314 0.508 0.547 0.536
SpeciesPorites compressa:Months35 0.434 -0.588 -0.324 -0.352 -0.352 -0.346 -0.345 -0.345 -0.776 0.438 0.464 0.458
BleachNon-bleach:Months12 0.518 -0.378 -0.681 -0.734 -0.438 -0.428 -0.425 -0.425 -0.333 0.499 0.524 0.309
BleachNon-bleach:Months17 0.518 -0.378 -0.681 -0.438 -0.734 -0.428 -0.425 -0.425 -0.333 0.499 0.313 0.518
BleachNon-bleach:Months20 0.513 -0.375 -0.672 -0.434 -0.434 -0.743 -0.420 -0.420 -0.332 0.493 0.310 0.306
BleachNon-bleach:Months24 0.502 -0.367 -0.658 -0.424 -0.424 -0.414 -0.733 -0.417 -0.325 0.483 0.303 0.300
BleachNon-bleach:Months29 0.502 -0.367 -0.658 -0.424 -0.424 -0.414 -0.417 -0.733 -0.325 0.483 0.303 0.300
BleachNon-bleach:Months35 0.441 -0.322 -0.572 -0.357 -0.357 -0.352 -0.350 -0.350 -0.788 0.420 0.255 0.252
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.368 0.497 0.483 0.521 0.311 0.304 0.302 0.302 0.236 -0.663 -0.731 -0.405
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.369 0.496 0.484 0.312 0.522 0.305 0.302 0.302 0.237 -0.661 -0.411 -0.740
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.367 0.495 0.481 0.310 0.310 0.532 0.301 0.301 0.237 -0.659 -0.412 -0.403
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.344 0.480 0.451 0.291 0.291 0.284 0.502 0.286 0.223 -0.640 -0.391 -0.381
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.352 0.488 0.461 0.297 0.297 0.290 0.292 0.513 0.228 -0.650 -0.399 -0.389
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.323 0.437 0.420 0.262 0.262 0.258 0.257 0.257 0.578 -0.571 -0.347 -0.341
SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M12 BN-:M17 BN-:M20 BN-:M24 BN-:M29 BN-:M3 SPc:BN-:M12
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24 0.530
SpeciesPorites compressa:Months29 0.540 0.532
SpeciesPorites compressa:Months35 0.461 0.447 0.456
BleachNon-bleach:Months12 0.310 0.295 0.300 0.258
BleachNon-bleach:Months17 0.310 0.295 0.300 0.258 0.566
BleachNon-bleach:Months20 0.538 0.291 0.297 0.257 0.559 0.559
BleachNon-bleach:Months24 0.300 0.508 0.295 0.252 0.548 0.548 0.541
BleachNon-bleach:Months29 0.300 0.289 0.518 0.252 0.548 0.548 0.541 0.537
BleachNon-bleach:Months35 0.255 0.242 0.247 0.612 0.459 0.459 0.455 0.449 0.449
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.409 -0.393 -0.400 -0.339 -0.710 -0.402 -0.397 -0.389 -0.389 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.406 -0.388 -0.396 -0.338 -0.403 -0.711 -0.398 -0.390 -0.390 -0.326 0.533
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.736 -0.391 -0.398 -0.338 -0.400 -0.400 -0.716 -0.387 -0.387 -0.326 0.535
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.386 -0.732 -0.393 -0.326 -0.375 -0.375 -0.371 -0.686 -0.368 -0.308 0.506
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.394 -0.394 -0.733 -0.334 -0.384 -0.384 -0.379 -0.376 -0.700 -0.314 0.517
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.345 -0.333 -0.340 -0.745 -0.337 -0.337 -0.334 -0.329 -0.329 -0.734 0.449
SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months12
SpeciesPorites compressa:BleachNon-bleach:Months17
SpeciesPorites compressa:BleachNon-bleach:Months20 0.530
SpeciesPorites compressa:BleachNon-bleach:Months24 0.500 0.503
SpeciesPorites compressa:BleachNon-bleach:Months29 0.511 0.513 0.508
SpeciesPorites compressa:BleachNon-bleach:Months35 0.447 0.447 0.427 0.438
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-3.348464786 -0.354082809 0.005359321 0.316483114 3.299113814
Number of Observations: 236
Number of Groups: 42 r.squaredGLMM(cs.lme) R2m R2c
[1,] 0.6089081 0.6983043####Coefficients
coef(cs.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months12 Months17 Months20 Months24 Months29 Months35
3 952.9915 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
4 725.5172 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
11 1053.7148 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
12 1295.5008 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
19 733.5192 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
20 739.0457 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
26 909.5442 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
27 882.9563 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
41 914.8362 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
42 909.7585 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
43 881.2889 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
44 921.8109 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
45 877.4851 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
46 881.5128 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
201 837.3597 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
202 989.5658 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
203 1168.4724 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
204 968.6623 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
209 740.9547 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
210 910.4040 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
211 709.1354 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
212 798.8933 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
213 1016.8532 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
214 938.5842 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
217 917.8969 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
218 836.5665 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
219 1016.8212 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
220 967.9980 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
221 878.3537 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
222 855.3350 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
225 903.1398 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
229 1017.8689 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
230 948.7124 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
235 907.4590 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
237 932.0321 -526.0491 322.115 -357.0817 30.47163 346.6183 10.16964 -54.79992 -106.1453
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months12 SpeciesPorites compressa:Months17
3 -332.9044 83.28831 -285.1716
4 -332.9044 83.28831 -285.1716
11 -332.9044 83.28831 -285.1716
12 -332.9044 83.28831 -285.1716
19 -332.9044 83.28831 -285.1716
20 -332.9044 83.28831 -285.1716
26 -332.9044 83.28831 -285.1716
27 -332.9044 83.28831 -285.1716
41 -332.9044 83.28831 -285.1716
42 -332.9044 83.28831 -285.1716
43 -332.9044 83.28831 -285.1716
44 -332.9044 83.28831 -285.1716
45 -332.9044 83.28831 -285.1716
46 -332.9044 83.28831 -285.1716
201 -332.9044 83.28831 -285.1716
202 -332.9044 83.28831 -285.1716
203 -332.9044 83.28831 -285.1716
204 -332.9044 83.28831 -285.1716
209 -332.9044 83.28831 -285.1716
210 -332.9044 83.28831 -285.1716
211 -332.9044 83.28831 -285.1716
212 -332.9044 83.28831 -285.1716
213 -332.9044 83.28831 -285.1716
214 -332.9044 83.28831 -285.1716
217 -332.9044 83.28831 -285.1716
218 -332.9044 83.28831 -285.1716
219 -332.9044 83.28831 -285.1716
220 -332.9044 83.28831 -285.1716
221 -332.9044 83.28831 -285.1716
222 -332.9044 83.28831 -285.1716
225 -332.9044 83.28831 -285.1716
229 -332.9044 83.28831 -285.1716
230 -332.9044 83.28831 -285.1716
235 -332.9044 83.28831 -285.1716
237 -332.9044 83.28831 -285.1716
SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35
3 -436.1449 -124.891 -80.05829 344.5779
4 -436.1449 -124.891 -80.05829 344.5779
11 -436.1449 -124.891 -80.05829 344.5779
12 -436.1449 -124.891 -80.05829 344.5779
19 -436.1449 -124.891 -80.05829 344.5779
20 -436.1449 -124.891 -80.05829 344.5779
26 -436.1449 -124.891 -80.05829 344.5779
27 -436.1449 -124.891 -80.05829 344.5779
41 -436.1449 -124.891 -80.05829 344.5779
42 -436.1449 -124.891 -80.05829 344.5779
43 -436.1449 -124.891 -80.05829 344.5779
44 -436.1449 -124.891 -80.05829 344.5779
45 -436.1449 -124.891 -80.05829 344.5779
46 -436.1449 -124.891 -80.05829 344.5779
201 -436.1449 -124.891 -80.05829 344.5779
202 -436.1449 -124.891 -80.05829 344.5779
203 -436.1449 -124.891 -80.05829 344.5779
204 -436.1449 -124.891 -80.05829 344.5779
209 -436.1449 -124.891 -80.05829 344.5779
210 -436.1449 -124.891 -80.05829 344.5779
211 -436.1449 -124.891 -80.05829 344.5779
212 -436.1449 -124.891 -80.05829 344.5779
213 -436.1449 -124.891 -80.05829 344.5779
214 -436.1449 -124.891 -80.05829 344.5779
217 -436.1449 -124.891 -80.05829 344.5779
218 -436.1449 -124.891 -80.05829 344.5779
219 -436.1449 -124.891 -80.05829 344.5779
220 -436.1449 -124.891 -80.05829 344.5779
221 -436.1449 -124.891 -80.05829 344.5779
222 -436.1449 -124.891 -80.05829 344.5779
225 -436.1449 -124.891 -80.05829 344.5779
229 -436.1449 -124.891 -80.05829 344.5779
230 -436.1449 -124.891 -80.05829 344.5779
235 -436.1449 -124.891 -80.05829 344.5779
237 -436.1449 -124.891 -80.05829 344.5779
BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20 BleachNon-bleach:Months24 BleachNon-bleach:Months29
3 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
4 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
11 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
12 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
19 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
20 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
26 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
27 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
41 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
42 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
43 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
44 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
45 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
46 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
201 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
202 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
203 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
204 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
209 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
210 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
211 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
212 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
213 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
214 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
217 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
218 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
219 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
220 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
221 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
222 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
225 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
229 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
230 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
235 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
237 -134.8073 -445.6604 -383.2454 25.53363 -270.3321
BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 -179.2011 151.0806 442.3094
4 -179.2011 151.0806 442.3094
11 -179.2011 151.0806 442.3094
12 -179.2011 151.0806 442.3094
19 -179.2011 151.0806 442.3094
20 -179.2011 151.0806 442.3094
26 -179.2011 151.0806 442.3094
27 -179.2011 151.0806 442.3094
41 -179.2011 151.0806 442.3094
42 -179.2011 151.0806 442.3094
43 -179.2011 151.0806 442.3094
44 -179.2011 151.0806 442.3094
45 -179.2011 151.0806 442.3094
46 -179.2011 151.0806 442.3094
201 -179.2011 151.0806 442.3094
202 -179.2011 151.0806 442.3094
203 -179.2011 151.0806 442.3094
204 -179.2011 151.0806 442.3094
209 -179.2011 151.0806 442.3094
210 -179.2011 151.0806 442.3094
211 -179.2011 151.0806 442.3094
212 -179.2011 151.0806 442.3094
213 -179.2011 151.0806 442.3094
214 -179.2011 151.0806 442.3094
217 -179.2011 151.0806 442.3094
218 -179.2011 151.0806 442.3094
219 -179.2011 151.0806 442.3094
220 -179.2011 151.0806 442.3094
221 -179.2011 151.0806 442.3094
222 -179.2011 151.0806 442.3094
225 -179.2011 151.0806 442.3094
229 -179.2011 151.0806 442.3094
230 -179.2011 151.0806 442.3094
235 -179.2011 151.0806 442.3094
237 -179.2011 151.0806 442.3094
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 443.1745 6.070277
4 443.1745 6.070277
11 443.1745 6.070277
12 443.1745 6.070277
19 443.1745 6.070277
20 443.1745 6.070277
26 443.1745 6.070277
27 443.1745 6.070277
41 443.1745 6.070277
42 443.1745 6.070277
43 443.1745 6.070277
44 443.1745 6.070277
45 443.1745 6.070277
46 443.1745 6.070277
201 443.1745 6.070277
202 443.1745 6.070277
203 443.1745 6.070277
204 443.1745 6.070277
209 443.1745 6.070277
210 443.1745 6.070277
211 443.1745 6.070277
212 443.1745 6.070277
213 443.1745 6.070277
214 443.1745 6.070277
217 443.1745 6.070277
218 443.1745 6.070277
219 443.1745 6.070277
220 443.1745 6.070277
221 443.1745 6.070277
222 443.1745 6.070277
225 443.1745 6.070277
229 443.1745 6.070277
230 443.1745 6.070277
235 443.1745 6.070277
237 443.1745 6.070277
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 282.1583 186.8777
4 282.1583 186.8777
11 282.1583 186.8777
12 282.1583 186.8777
19 282.1583 186.8777
20 282.1583 186.8777
26 282.1583 186.8777
27 282.1583 186.8777
41 282.1583 186.8777
42 282.1583 186.8777
43 282.1583 186.8777
44 282.1583 186.8777
45 282.1583 186.8777
46 282.1583 186.8777
201 282.1583 186.8777
202 282.1583 186.8777
203 282.1583 186.8777
204 282.1583 186.8777
209 282.1583 186.8777
210 282.1583 186.8777
211 282.1583 186.8777
212 282.1583 186.8777
213 282.1583 186.8777
214 282.1583 186.8777
217 282.1583 186.8777
218 282.1583 186.8777
219 282.1583 186.8777
220 282.1583 186.8777
221 282.1583 186.8777
222 282.1583 186.8777
225 282.1583 186.8777
229 282.1583 186.8777
230 282.1583 186.8777
235 282.1583 186.8777
237 282.1583 186.8777
[ reached 'max' / getOption("max.print") -- omitted 7 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
csfig<-ggplot(phys, aes(y=Citrate.synthase.mU.mg.protein.1, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_wrap(~Species, scales="free")+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
csfig
csfig2<-ggplot(phys, aes(y=Citrate.synthase.mU.mg.protein.1, x=Sym.density_10.6cells.cm.2, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="lm")+
facet_grid(~Species)+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
csfig2 ##this follows the patterns seen in Hawkins et al 2016
csfig3<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="lm")+
#geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
facet_wrap(~Species, scales = "free")+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
csfig3 ##this follows the patterns seen in Hawkins et al 2016
csfig3<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="lm")+
#geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
facet_wrap(~Species, scales = "free")+
scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
scale_x_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
csfig3 ##this follows the patterns seen in Hawkins et al 2016
csfig4<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1))+
geom_point(aes(color=Bleach),alpha=0.4)+
geom_smooth(method="lm",color = 'black',)+
#geom_hline(yintercept = 0, linetype="solid", size=0.7, show.legend = TRUE)+
#facet_wrap(~Species, scales = "free")+
scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
scale_x_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
csfig4 ##this follows the patterns seen in Hawkins et al 2016
csfigs<-cowplot::plot_grid(csfig4, csfig3, nrow = 1, ncol = 2, rel_heights = c(1,2.5), labels=c('(a)','(b)'))`geom_smooth()` using formula 'y ~ x'
Warning: Removed 252 rows containing non-finite values (stat_smooth).Warning: Removed 252 rows containing missing values (geom_point).`geom_smooth()` using formula 'y ~ x'
Warning: Removed 252 rows containing non-finite values (stat_smooth).Warning: Removed 252 rows containing missing values (geom_point).csfigs
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
cs_stress_fig<-ggplot(phys_stress, aes(y=Citrate.synthase.mU.mg.protein.1, x=Months, color=Bleach, fill=Bleach))+
geom_boxplot(alpha=0.6)+
#geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
#geom_point(size=1.5, position= pd)+
#geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(CS~Specific~Activity~(U~'\U2219'~mg~protein^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
cs_stress_fig
library(Rmisc)
cs_sum<-summarySE(phys, measurevar='Citrate.synthase.mU.mg.protein.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedcs_sumsym.lme <- lme(Sym.density_10.6cells.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
Anova(sym.lme, type=3)Analysis of Deviance Table (Type III tests)
Response: Sym.density_10.6cells.cm.2
Chisq Df Pr(>Chisq)
(Intercept) 1.3357 1 0.24779
Species 2.0611 1 0.15111
Bleach 1.1467 1 0.28424
Months 14.9134 7 0.03713 *
Species:Bleach 0.7858 1 0.37539
Species:Months 16.3885 7 0.02179 *
Bleach:Months 1.2918 7 0.98866
Species:Bleach:Months 3.8918 7 0.79215
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(sym.lme, list(pairwise ~ Species:Bleach), adjust = "tukey", simple="Bleach")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Bleach`
Species Bleach emmean SE df lower.CL upper.CL
Montipora capitata Bleach 1.36 0.152 43 1.05 1.67
Porites compressa Bleach 2.78 0.149 42 2.48 3.08
Montipora capitata Non-bleach 1.97 0.144 43 1.68 2.26
Porites compressa Non-bleach 2.65 0.150 42 2.35 2.96
Results are averaged over the levels of: Months
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Bleach | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -0.612 0.209 202 -2.922 0.0039
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 0.125 0.207 202 0.604 0.5463
Results are averaged over the levels of: Months
Degrees-of-freedom method: containment csfigs<-cowplot::plot_grid(csfig, csfig2, nrow = 2, ncol = 1)Warning: Removed 80 rows containing non-finite values (stat_smooth).Warning: Removed 80 rows containing missing values (geom_point).`geom_smooth()` using formula 'y ~ x'
Warning: Removed 80 rows containing non-finite values (stat_smooth).Warning: Removed 80 rows containing missing values (geom_point).csfigs
##Symbiont density ###Normality
hist(phys$Sym.density_10.6cells.cm.2)
sym.lm<- lm(Sym.density_10.6cells.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(sym.lm, ask=FALSE, which=1:6)
###Stats
sym.lme <- lme(Sym.density_10.6cells.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(sym.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Sym.density_10.6cells.cm.2
Chisq Df Pr(>Chisq)
(Intercept) 1.3357 1 0.24779
Species 2.0611 1 0.15111
Bleach 1.1467 1 0.28424
Months 14.9134 7 0.03713 *
Species:Bleach 0.7858 1 0.37539
Species:Months 16.3885 7 0.02179 *
Bleach:Months 1.2918 7 0.98866
Species:Bleach:Months 3.8918 7 0.79215
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(sym.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 0.619 0.229 43 0.158 1.08
Porites compressa 0 0.989 0.229 42 0.527 1.45
Montipora capitata 10 1.523 0.257 43 1.004 2.04
Porites compressa 10 2.979 0.243 42 2.490 3.47
Montipora capitata 12 1.438 0.229 43 0.977 1.90
Porites compressa 12 2.082 0.241 42 1.595 2.57
Montipora capitata 17 1.677 0.229 43 1.216 2.14
Porites compressa 17 3.554 0.243 42 3.064 4.04
Montipora capitata 20 1.758 0.235 43 1.285 2.23
Porites compressa 20 2.731 0.241 42 2.244 3.22
Montipora capitata 24 1.729 0.241 43 1.243 2.21
Porites compressa 24 3.626 0.273 42 3.076 4.18
Montipora capitata 29 2.139 0.241 43 1.653 2.62
Porites compressa 29 2.782 0.255 42 2.266 3.30
Montipora capitata 35 2.442 0.319 43 1.799 3.08
Porites compressa 35 2.989 0.298 42 2.388 3.59
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months0 - Months10 -0.9041 0.333 202 -2.716 0.1239
Months0 - Months12 -0.8196 0.311 202 -2.631 0.1510
Months0 - Months17 -1.0582 0.311 202 -3.397 0.0183
Months0 - Months20 -1.1395 0.316 202 -3.606 0.0092
Months0 - Months24 -1.1101 0.321 202 -3.463 0.0148
Months0 - Months29 -1.5203 0.321 202 -4.743 0.0001
Months0 - Months35 -1.8228 0.384 202 -4.741 0.0001
Months10 - Months12 0.0845 0.333 202 0.254 1.0000
Months10 - Months17 -0.1541 0.333 202 -0.463 0.9998
Months10 - Months20 -0.2354 0.337 202 -0.698 0.9970
Months10 - Months24 -0.2060 0.340 202 -0.605 0.9988
Months10 - Months29 -0.6162 0.340 202 -1.810 0.6141
Months10 - Months35 -0.9187 0.402 202 -2.287 0.3061
Months12 - Months17 -0.2386 0.311 202 -0.766 0.9946
Months12 - Months20 -0.3199 0.316 202 -1.012 0.9722
Months12 - Months24 -0.2905 0.321 202 -0.906 0.9852
Months12 - Months29 -0.7007 0.321 202 -2.186 0.3646
Months12 - Months35 -1.0032 0.384 202 -2.610 0.1586
Months17 - Months20 -0.0813 0.316 202 -0.257 1.0000
Months17 - Months24 -0.0519 0.321 202 -0.162 1.0000
Months17 - Months29 -0.4621 0.321 202 -1.442 0.8367
Months17 - Months35 -0.7646 0.384 202 -1.989 0.4920
Months20 - Months24 0.0294 0.325 202 0.091 1.0000
Months20 - Months29 -0.3808 0.325 202 -1.172 0.9391
Months20 - Months35 -0.6832 0.388 202 -1.762 0.6466
Months24 - Months29 -0.4102 0.328 202 -1.249 0.9159
Months24 - Months35 -0.7127 0.391 202 -1.822 0.6058
Months29 - Months35 -0.3025 0.391 202 -0.773 0.9943
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months0 - Months10 -1.9907 0.322 202 -6.187 <.0001
Months0 - Months12 -1.0931 0.321 202 -3.409 0.0176
Months0 - Months17 -2.5651 0.322 202 -7.972 <.0001
Months0 - Months20 -1.7420 0.321 202 -5.433 <.0001
Months0 - Months24 -2.6370 0.345 202 -7.643 <.0001
Months0 - Months29 -1.7930 0.332 202 -5.408 <.0001
Months0 - Months35 -2.0007 0.367 202 -5.454 <.0001
Months10 - Months12 0.8976 0.329 202 2.725 0.1212
Months10 - Months17 -0.5745 0.330 202 -1.739 0.6618
Months10 - Months20 0.2487 0.329 202 0.755 0.9951
Months10 - Months24 -0.6464 0.353 202 -1.830 0.6005
Months10 - Months29 0.1977 0.340 202 0.581 0.9991
Months10 - Months35 -0.0101 0.375 202 -0.027 1.0000
Months12 - Months17 -1.4721 0.329 202 -4.469 0.0003
Months12 - Months20 -0.6489 0.328 202 -1.976 0.5004
Months12 - Months24 -1.5440 0.352 202 -4.384 0.0005
Months12 - Months29 -0.6999 0.339 202 -2.065 0.4414
Months12 - Months35 -0.9077 0.374 202 -2.429 0.2333
Months17 - Months20 0.8232 0.329 202 2.499 0.2020
Months17 - Months24 -0.0719 0.353 202 -0.203 1.0000
Months17 - Months29 0.7722 0.340 202 2.271 0.3151
Months17 - Months35 0.5644 0.375 202 1.506 0.8034
Months20 - Months24 -0.8950 0.352 202 -2.541 0.1843
Months20 - Months29 -0.0510 0.339 202 -0.150 1.0000
Months20 - Months35 -0.2587 0.374 202 -0.692 0.9971
Months24 - Months29 0.8440 0.361 202 2.337 0.2787
Months24 - Months35 0.6363 0.395 202 1.613 0.7423
Months29 - Months35 -0.2077 0.382 202 -0.543 0.9994
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 8 estimates summary(sym.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.276743 0.9849971
Fixed effects: Sym.density_10.6cells.cm.2 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.708
BleachNon-bleach -0.707 0.500
Months10 -0.615 0.435 0.435
Months12 -0.681 0.482 0.481 0.452
Months17 -0.681 0.482 0.481 0.452 0.500
Months20 -0.662 0.468 0.468 0.438 0.486 0.486
Months24 -0.662 0.468 0.468 0.442 0.486 0.486 0.472
Months29 -0.662 0.468 0.468 0.442 0.486 0.486 0.472 0.475
Months35 -0.516 0.365 0.365 0.335 0.372 0.372 0.363 0.363 0.363
SpeciesPorites compressa:BleachNon-bleach 0.501 -0.707 -0.708 -0.308 -0.341 -0.341 -0.331 -0.331 -0.331 -0.258
SpeciesPorites compressa:Months10 0.443 -0.627 -0.313 -0.721 -0.326 -0.326 -0.316 -0.318 -0.318 -0.242 0.444
SpeciesPorites compressa:Months12 0.474 -0.672 -0.335 -0.315 -0.697 -0.348 -0.339 -0.339 -0.339 -0.259 0.475 0.456
SpeciesPorites compressa:Months17 0.466 -0.660 -0.330 -0.309 -0.342 -0.685 -0.333 -0.333 -0.333 -0.254 0.467 0.449
SpeciesPorites compressa:Months20 0.468 -0.662 -0.331 -0.309 -0.344 -0.344 -0.707 -0.334 -0.334 -0.256 0.469 0.449
SpeciesPorites compressa:Months24 0.450 -0.640 -0.318 -0.300 -0.330 -0.330 -0.321 -0.680 -0.323 -0.247 0.455 0.432
SpeciesPorites compressa:Months29 0.459 -0.653 -0.325 -0.307 -0.337 -0.337 -0.328 -0.330 -0.694 -0.252 0.464 0.442
SpeciesPorites compressa:Months35 0.397 -0.562 -0.281 -0.258 -0.286 -0.286 -0.279 -0.279 -0.279 -0.770 0.397 0.374
BleachNon-bleach:Months10 0.450 -0.319 -0.637 -0.733 -0.331 -0.331 -0.321 -0.324 -0.324 -0.245 0.451 0.528
BleachNon-bleach:Months12 0.481 -0.341 -0.681 -0.319 -0.707 -0.354 -0.344 -0.344 -0.344 -0.263 0.482 0.230
BleachNon-bleach:Months17 0.481 -0.341 -0.681 -0.319 -0.354 -0.707 -0.344 -0.344 -0.344 -0.263 0.482 0.230
BleachNon-bleach:Months20 0.475 -0.336 -0.671 -0.314 -0.348 -0.348 -0.717 -0.338 -0.338 -0.260 0.475 0.226
BleachNon-bleach:Months24 0.468 -0.331 -0.662 -0.312 -0.344 -0.344 -0.334 -0.707 -0.336 -0.257 0.469 0.225
BleachNon-bleach:Months29 0.468 -0.331 -0.662 -0.312 -0.344 -0.344 -0.334 -0.336 -0.707 -0.257 0.469 0.225
BleachNon-bleach:Months35 0.398 -0.281 -0.560 -0.258 -0.286 -0.286 -0.280 -0.280 -0.280 -0.771 0.396 0.186
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.324 0.459 0.458 0.526 0.238 0.238 0.230 0.232 0.232 0.176 -0.650 -0.731
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.335 0.475 0.474 0.222 0.493 0.246 0.239 0.239 0.239 0.183 -0.672 -0.322
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.334 0.475 0.473 0.222 0.246 0.491 0.239 0.239 0.239 0.183 -0.672 -0.323
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.333 0.472 0.471 0.220 0.245 0.245 0.503 0.238 0.238 0.183 -0.667 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.317 0.454 0.449 0.212 0.233 0.233 0.226 0.480 0.228 0.174 -0.642 -0.305
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.324 0.463 0.459 0.216 0.238 0.238 0.231 0.233 0.490 0.178 -0.655 -0.312
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.288 0.407 0.405 0.187 0.207 0.207 0.202 0.202 0.202 0.558 -0.572 -0.271
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.479
SpeciesPorites compressa:Months20 0.481 0.472
SpeciesPorites compressa:Months24 0.462 0.453 0.455
SpeciesPorites compressa:Months29 0.472 0.463 0.465 0.454
SpeciesPorites compressa:Months35 0.400 0.394 0.395 0.382 0.390
BleachNon-bleach:Months10 0.230 0.227 0.227 0.220 0.225 0.189
BleachNon-bleach:Months12 0.493 0.242 0.243 0.233 0.238 0.202 0.468
BleachNon-bleach:Months17 0.246 0.484 0.243 0.233 0.238 0.202 0.468 0.500
BleachNon-bleach:Months20 0.243 0.239 0.507 0.230 0.235 0.200 0.460 0.493 0.493
BleachNon-bleach:Months24 0.239 0.235 0.236 0.480 0.233 0.197 0.458 0.486 0.486 0.479
BleachNon-bleach:Months29 0.239 0.235 0.236 0.228 0.491 0.197 0.458 0.486 0.486 0.479 0.475
BleachNon-bleach:Months35 0.200 0.196 0.198 0.190 0.194 0.593 0.380 0.405 0.405 0.400 0.396
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.332 -0.329 -0.327 -0.315 -0.322 -0.274 -0.718 -0.336 -0.336 -0.331 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.707 -0.339 -0.340 -0.326 -0.333 -0.283 -0.326 -0.697 -0.348 -0.343 -0.339
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.344 -0.718 -0.339 -0.325 -0.332 -0.283 -0.325 -0.347 -0.695 -0.342 -0.338
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.342 -0.336 -0.712 -0.324 -0.331 -0.281 -0.323 -0.346 -0.346 -0.702 -0.336
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.326 -0.319 -0.321 -0.708 -0.322 -0.270 -0.310 -0.330 -0.330 -0.325 -0.678
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.333 -0.327 -0.328 -0.322 -0.708 -0.276 -0.317 -0.337 -0.337 -0.332 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.290 -0.285 -0.286 -0.275 -0.282 -0.725 -0.275 -0.293 -0.293 -0.290 -0.286
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.396
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.329 -0.273
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.339 -0.282 0.470
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.338 -0.281 0.471 0.486
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.336 -0.281 0.466 0.484 0.482
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 -0.269 0.445 0.461 0.459 0.457
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.693 -0.274 0.455 0.471 0.469 0.467 0.455
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.286 -0.723 0.397 0.410 0.410 0.407 0.389 0.399
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.65603853 -0.48359457 -0.01075316 0.41785354 5.92981321
Number of Observations: 276
Number of Groups: 44 Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d hh:mm:ss'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d hh:mm:ss'r.squaredGLMM(sym.lme) R2m R2c
[1,] 0.4338455 0.4752666res <- cor.test(phys$Months, phys$Sym.density_10.6cells.cm.2,
method = "pearson")Error in cor.test.default(phys$Months, phys$Sym.density_10.6cells.cm.2, :
'x' must be a numeric vector####Coefficients
coef(sym.lme)###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
symfig<-ggplot(phys, aes(y=Sym.density_10.6cells.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})), limits=c(-0,5))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
symfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
sym_stress_fig<-ggplot(phys_stress, aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
geom_boxplot(alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})), limits=c(0,5))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
sym_stress_fig
library(Rmisc)
sym_sum<-summarySE(phys, measurevar='Sym.density_10.6cells.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
sym_sumsymfig_3<-ggplot(sym_sum, aes(y=Sym.density_10.6cells.cm.2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=sym_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "sym", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Sym.density_10.6cells.cm.2-se, ymax=Sym.density_10.6cells.cm.2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statsymfig_3
lmfig<-ggplot(phys, aes(y=Sym.density_10.6cells.cm.2, x=AFDW_mg.cm.2, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="lm")+
#facet_grid(~Species)+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
lmfig ##this follows the patterns seen in Hawkins et al 2016
##Chlorphyll a ###Normality
hist(phys$Chl.a_ug.cm2)
chla.lm<- lm(Chl.a_ug.cm2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(chla.lm, ask=FALSE, which=1:6)
###Stats
chla.lme <- lme(Chl.a_ug.cm2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(chla.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Chl.a_ug.cm2
Chisq Df Pr(>Chisq)
(Intercept) 5.8611 1 0.0154795 *
Species 46.7985 1 7.867e-12 ***
Bleach 0.9625 1 0.3265554
Months 24.5860 7 0.0008983 ***
Species:Bleach 1.4954 1 0.2213852
Species:Months 12.5854 7 0.0828781 .
Bleach:Months 2.2491 7 0.9447760
Species:Bleach:Months 14.9629 7 0.0364776 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(chla.lme, list(pairwise ~ Months), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Months`
Months emmean SE df lower.CL upper.CL
0 12.0 0.815 42 10.31 13.6
10 10.0 0.889 42 8.25 11.8
12 14.8 0.837 42 13.07 16.4
17 20.1 0.840 42 18.39 21.8
20 13.4 0.847 42 11.65 15.1
24 15.9 0.914 42 14.04 17.7
29 17.3 0.883 42 15.55 19.1
35 10.6 1.091 42 8.42 12.8
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Months`
1 estimate SE df t.ratio p.value
Months0 - Months10 1.905 1.14 202 1.678 0.7015
Months0 - Months12 -2.804 1.10 202 -2.560 0.1771
Months0 - Months17 -8.136 1.10 202 -7.415 <.0001
Months0 - Months20 -1.410 1.10 202 -1.278 0.9059
Months0 - Months24 -3.929 1.16 202 -3.402 0.0180
Months0 - Months29 -5.379 1.13 202 -4.757 0.0001
Months0 - Months35 1.327 1.31 202 1.013 0.9721
Months10 - Months12 -4.709 1.15 202 -4.103 0.0015
Months10 - Months17 -10.041 1.15 202 -8.737 <.0001
Months10 - Months20 -3.315 1.16 202 -2.868 0.0847
Months10 - Months24 -5.834 1.20 202 -4.852 0.0001
Months10 - Months29 -7.284 1.18 202 -6.177 <.0001
Months10 - Months35 -0.578 1.35 202 -0.427 0.9999
Months12 - Months17 -5.332 1.11 202 -4.804 0.0001
Months12 - Months20 1.394 1.12 202 1.249 0.9160
Months12 - Months24 -1.126 1.17 202 -0.965 0.9788
Months12 - Months29 -2.575 1.14 202 -2.253 0.3253
Months12 - Months35 4.130 1.32 202 3.127 0.0417
Months17 - Months20 6.726 1.12 202 6.016 <.0001
Months17 - Months24 4.207 1.17 202 3.598 0.0095
Months17 - Months29 2.757 1.15 202 2.408 0.2434
Months17 - Months35 9.463 1.32 202 7.153 <.0001
Months20 - Months24 -2.519 1.17 202 -2.144 0.3903
Months20 - Months29 -3.969 1.15 202 -3.448 0.0155
Months20 - Months35 2.737 1.33 202 2.063 0.4428
Months24 - Months29 -1.449 1.20 202 -1.212 0.9275
Months24 - Months35 5.256 1.37 202 3.840 0.0040
Months29 - Months35 6.705 1.35 202 4.980 <.0001
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 8 estimates summary(chla.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 7.10234 5.52933
Fixed effects: pg.Chl.a.per.zoox ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.732
BleachNon-bleach -0.707 0.518
Months10 -0.395 0.289 0.279
Months12 -0.442 0.323 0.312 0.447
Months17 -0.442 0.323 0.312 0.447 0.500
Months20 -0.428 0.314 0.303 0.430 0.485 0.485
Months24 -0.428 0.313 0.303 0.443 0.484 0.484 0.468
Months29 -0.428 0.313 0.303 0.443 0.484 0.484 0.468 0.480
Months35 -0.361 0.264 0.255 0.307 0.343 0.343 0.338 0.339 0.339
SpeciesPorites compressa:BleachNon-bleach 0.545 -0.676 -0.771 -0.215 -0.241 -0.241 -0.234 -0.233 -0.233 -0.197
SpeciesPorites compressa:Months10 0.280 -0.440 -0.198 -0.708 -0.317 -0.317 -0.304 -0.314 -0.314 -0.217 0.327
SpeciesPorites compressa:Months12 0.294 -0.469 -0.208 -0.298 -0.667 -0.333 -0.323 -0.323 -0.323 -0.229 0.353 0.468
SpeciesPorites compressa:Months17 0.295 -0.463 -0.208 -0.299 -0.334 -0.667 -0.323 -0.323 -0.323 -0.229 0.345 0.473
SpeciesPorites compressa:Months20 0.296 -0.468 -0.210 -0.297 -0.335 -0.335 -0.691 -0.323 -0.323 -0.233 0.351 0.468
SpeciesPorites compressa:Months24 0.282 -0.464 -0.200 -0.293 -0.319 -0.319 -0.309 -0.660 -0.317 -0.224 0.360 0.451
SpeciesPorites compressa:Months29 0.289 -0.471 -0.204 -0.299 -0.327 -0.327 -0.316 -0.324 -0.675 -0.229 0.364 0.462
SpeciesPorites compressa:Months35 0.274 -0.420 -0.194 -0.234 -0.261 -0.261 -0.257 -0.258 -0.258 -0.761 0.304 0.370
BleachNon-bleach:Months10 0.290 -0.212 -0.411 -0.734 -0.328 -0.328 -0.316 -0.326 -0.326 -0.225 0.317 0.520
BleachNon-bleach:Months12 0.312 -0.229 -0.442 -0.316 -0.707 -0.354 -0.343 -0.342 -0.342 -0.243 0.341 0.224
BleachNon-bleach:Months17 0.312 -0.229 -0.442 -0.316 -0.354 -0.707 -0.343 -0.342 -0.342 -0.243 0.341 0.224
BleachNon-bleach:Months20 0.308 -0.225 -0.435 -0.308 -0.348 -0.348 -0.718 -0.336 -0.336 -0.242 0.335 0.218
BleachNon-bleach:Months24 0.303 -0.221 -0.428 -0.314 -0.342 -0.342 -0.331 -0.707 -0.339 -0.240 0.330 0.222
BleachNon-bleach:Months29 0.303 -0.221 -0.428 -0.314 -0.342 -0.342 -0.331 -0.339 -0.707 -0.240 0.330 0.222
BleachNon-bleach:Months35 0.283 -0.207 -0.385 -0.241 -0.269 -0.269 -0.265 -0.266 -0.266 -0.784 0.296 0.170
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.206 0.333 0.291 0.520 0.233 0.233 0.224 0.231 0.231 0.160 -0.481 -0.737
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.210 0.338 0.297 0.213 0.476 0.238 0.231 0.230 0.230 0.163 -0.486 -0.334
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.213 0.346 0.301 0.216 0.241 0.482 0.234 0.233 0.233 0.166 -0.498 -0.344
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.213 0.339 0.301 0.213 0.241 0.241 0.497 0.232 0.232 0.168 -0.489 -0.336
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.200 0.342 0.284 0.208 0.227 0.227 0.219 0.468 0.225 0.159 -0.494 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.205 0.346 0.290 0.213 0.232 0.232 0.224 0.230 0.480 0.163 -0.500 -0.327
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.205 0.317 0.278 0.174 0.195 0.195 0.191 0.192 0.192 0.567 -0.429 -0.276
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.493
SpeciesPorites compressa:Months20 0.495 0.496
SpeciesPorites compressa:Months24 0.480 0.471 0.474
SpeciesPorites compressa:Months29 0.490 0.482 0.485 0.486
SpeciesPorites compressa:Months35 0.392 0.391 0.392 0.382 0.392
BleachNon-bleach:Months10 0.219 0.219 0.218 0.215 0.220 0.172
BleachNon-bleach:Months12 0.471 0.236 0.237 0.226 0.231 0.185 0.465
BleachNon-bleach:Months17 0.236 0.472 0.237 0.226 0.231 0.185 0.465 0.500
BleachNon-bleach:Months20 0.232 0.232 0.496 0.222 0.227 0.184 0.455 0.492 0.492
BleachNon-bleach:Months24 0.228 0.228 0.229 0.467 0.229 0.182 0.460 0.484 0.484 0.476
BleachNon-bleach:Months29 0.228 0.228 0.229 0.224 0.478 0.182 0.460 0.484 0.484 0.476 0.480
BleachNon-bleach:Months35 0.179 0.180 0.183 0.176 0.180 0.596 0.358 0.381 0.381 0.377 0.376
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.343 -0.350 -0.344 -0.332 -0.340 -0.274 -0.708 -0.329 -0.329 -0.322 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.713 -0.352 -0.353 -0.341 -0.349 -0.280 -0.313 -0.673 -0.336 -0.331 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.356 -0.725 -0.358 -0.340 -0.348 -0.284 -0.317 -0.341 -0.682 -0.336 -0.330
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.356 -0.356 -0.718 -0.340 -0.348 -0.282 -0.315 -0.340 -0.340 -0.692 -0.329
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.340 -0.333 -0.336 -0.717 -0.352 -0.274 -0.305 -0.320 -0.320 -0.315 -0.662
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.348 -0.341 -0.344 -0.352 -0.717 -0.281 -0.312 -0.328 -0.328 -0.323 -0.325
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.292 -0.291 -0.292 -0.282 -0.290 -0.746 -0.259 -0.275 -0.275 -0.273 -0.272
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.376
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.326 -0.253
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.326 -0.256 0.474
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.330 -0.260 0.488 0.491
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.329 -0.261 0.479 0.490 0.497
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.318 -0.249 0.456 0.463 0.467 0.466
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.678 -0.255 0.467 0.475 0.478 0.478 0.482
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.272 -0.723 0.394 0.402 0.406 0.404 0.386 0.397
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.17246879 -0.41809968 -0.03744327 0.27190526 4.27007839
Number of Observations: 273
Number of Groups: 44 r.squaredGLMM(chla.lme) R2m R2c
[1,] 0.2242011 0.7072347####Coefficients
coef(chla.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 13.714006 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
4 11.577017 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
11 11.011482 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
12 11.838750 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
19 15.213930 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
20 11.632791 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
26 11.755004 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
27 11.975038 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
35 5.272630 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
36 52.166466 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
41 17.620276 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
42 9.571929 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
43 10.259605 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
44 10.029119 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
45 10.835940 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
46 7.335088 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
201 13.519692 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
202 12.277872 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
203 12.577198 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
204 13.524240 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
209 11.370271 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
210 14.666687 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
211 12.452298 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
212 11.754798 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
213 14.343118 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
214 12.784725 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
217 15.915556 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
218 14.488540 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
219 11.275610 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
220 13.134052 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
221 13.929957 7.81891 -5.729839 -8.470467 -6.694 -3.41 -6.497333 -6.539383 -6.644938 -10.29917
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 8.733789 -5.827062 0.2904869
4 8.733789 -5.827062 0.2904869
11 8.733789 -5.827062 0.2904869
12 8.733789 -5.827062 0.2904869
19 8.733789 -5.827062 0.2904869
20 8.733789 -5.827062 0.2904869
26 8.733789 -5.827062 0.2904869
27 8.733789 -5.827062 0.2904869
35 8.733789 -5.827062 0.2904869
36 8.733789 -5.827062 0.2904869
41 8.733789 -5.827062 0.2904869
42 8.733789 -5.827062 0.2904869
43 8.733789 -5.827062 0.2904869
44 8.733789 -5.827062 0.2904869
45 8.733789 -5.827062 0.2904869
46 8.733789 -5.827062 0.2904869
201 8.733789 -5.827062 0.2904869
202 8.733789 -5.827062 0.2904869
203 8.733789 -5.827062 0.2904869
204 8.733789 -5.827062 0.2904869
209 8.733789 -5.827062 0.2904869
210 8.733789 -5.827062 0.2904869
211 8.733789 -5.827062 0.2904869
212 8.733789 -5.827062 0.2904869
213 8.733789 -5.827062 0.2904869
214 8.733789 -5.827062 0.2904869
217 8.733789 -5.827062 0.2904869
218 8.733789 -5.827062 0.2904869
219 8.733789 -5.827062 0.2904869
220 8.733789 -5.827062 0.2904869
221 8.733789 -5.827062 0.2904869
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 -10.70628 -7.599206 -7.081133 -3.997321
4 -10.70628 -7.599206 -7.081133 -3.997321
11 -10.70628 -7.599206 -7.081133 -3.997321
12 -10.70628 -7.599206 -7.081133 -3.997321
19 -10.70628 -7.599206 -7.081133 -3.997321
20 -10.70628 -7.599206 -7.081133 -3.997321
26 -10.70628 -7.599206 -7.081133 -3.997321
27 -10.70628 -7.599206 -7.081133 -3.997321
35 -10.70628 -7.599206 -7.081133 -3.997321
36 -10.70628 -7.599206 -7.081133 -3.997321
41 -10.70628 -7.599206 -7.081133 -3.997321
42 -10.70628 -7.599206 -7.081133 -3.997321
43 -10.70628 -7.599206 -7.081133 -3.997321
44 -10.70628 -7.599206 -7.081133 -3.997321
45 -10.70628 -7.599206 -7.081133 -3.997321
46 -10.70628 -7.599206 -7.081133 -3.997321
201 -10.70628 -7.599206 -7.081133 -3.997321
202 -10.70628 -7.599206 -7.081133 -3.997321
203 -10.70628 -7.599206 -7.081133 -3.997321
204 -10.70628 -7.599206 -7.081133 -3.997321
209 -10.70628 -7.599206 -7.081133 -3.997321
210 -10.70628 -7.599206 -7.081133 -3.997321
211 -10.70628 -7.599206 -7.081133 -3.997321
212 -10.70628 -7.599206 -7.081133 -3.997321
213 -10.70628 -7.599206 -7.081133 -3.997321
214 -10.70628 -7.599206 -7.081133 -3.997321
217 -10.70628 -7.599206 -7.081133 -3.997321
218 -10.70628 -7.599206 -7.081133 -3.997321
219 -10.70628 -7.599206 -7.081133 -3.997321
220 -10.70628 -7.599206 -7.081133 -3.997321
221 -10.70628 -7.599206 -7.081133 -3.997321
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -4.703357 8.053656 5.567 2.913 3.712333
4 -4.703357 8.053656 5.567 2.913 3.712333
11 -4.703357 8.053656 5.567 2.913 3.712333
12 -4.703357 8.053656 5.567 2.913 3.712333
19 -4.703357 8.053656 5.567 2.913 3.712333
20 -4.703357 8.053656 5.567 2.913 3.712333
26 -4.703357 8.053656 5.567 2.913 3.712333
27 -4.703357 8.053656 5.567 2.913 3.712333
35 -4.703357 8.053656 5.567 2.913 3.712333
36 -4.703357 8.053656 5.567 2.913 3.712333
41 -4.703357 8.053656 5.567 2.913 3.712333
42 -4.703357 8.053656 5.567 2.913 3.712333
43 -4.703357 8.053656 5.567 2.913 3.712333
44 -4.703357 8.053656 5.567 2.913 3.712333
45 -4.703357 8.053656 5.567 2.913 3.712333
46 -4.703357 8.053656 5.567 2.913 3.712333
201 -4.703357 8.053656 5.567 2.913 3.712333
202 -4.703357 8.053656 5.567 2.913 3.712333
203 -4.703357 8.053656 5.567 2.913 3.712333
204 -4.703357 8.053656 5.567 2.913 3.712333
209 -4.703357 8.053656 5.567 2.913 3.712333
210 -4.703357 8.053656 5.567 2.913 3.712333
211 -4.703357 8.053656 5.567 2.913 3.712333
212 -4.703357 8.053656 5.567 2.913 3.712333
213 -4.703357 8.053656 5.567 2.913 3.712333
214 -4.703357 8.053656 5.567 2.913 3.712333
217 -4.703357 8.053656 5.567 2.913 3.712333
218 -4.703357 8.053656 5.567 2.913 3.712333
219 -4.703357 8.053656 5.567 2.913 3.712333
220 -4.703357 8.053656 5.567 2.913 3.712333
221 -4.703357 8.053656 5.567 2.913 3.712333
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 3.99146 4.038127 4.802768 -5.05245
4 3.99146 4.038127 4.802768 -5.05245
11 3.99146 4.038127 4.802768 -5.05245
12 3.99146 4.038127 4.802768 -5.05245
19 3.99146 4.038127 4.802768 -5.05245
20 3.99146 4.038127 4.802768 -5.05245
26 3.99146 4.038127 4.802768 -5.05245
27 3.99146 4.038127 4.802768 -5.05245
35 3.99146 4.038127 4.802768 -5.05245
36 3.99146 4.038127 4.802768 -5.05245
41 3.99146 4.038127 4.802768 -5.05245
42 3.99146 4.038127 4.802768 -5.05245
43 3.99146 4.038127 4.802768 -5.05245
44 3.99146 4.038127 4.802768 -5.05245
45 3.99146 4.038127 4.802768 -5.05245
46 3.99146 4.038127 4.802768 -5.05245
201 3.99146 4.038127 4.802768 -5.05245
202 3.99146 4.038127 4.802768 -5.05245
203 3.99146 4.038127 4.802768 -5.05245
204 3.99146 4.038127 4.802768 -5.05245
209 3.99146 4.038127 4.802768 -5.05245
210 3.99146 4.038127 4.802768 -5.05245
211 3.99146 4.038127 4.802768 -5.05245
212 3.99146 4.038127 4.802768 -5.05245
213 3.99146 4.038127 4.802768 -5.05245
214 3.99146 4.038127 4.802768 -5.05245
217 3.99146 4.038127 4.802768 -5.05245
218 3.99146 4.038127 4.802768 -5.05245
219 3.99146 4.038127 4.802768 -5.05245
220 3.99146 4.038127 4.802768 -5.05245
221 3.99146 4.038127 4.802768 -5.05245
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 -7.412417 -0.2930444
4 -7.412417 -0.2930444
11 -7.412417 -0.2930444
12 -7.412417 -0.2930444
19 -7.412417 -0.2930444
20 -7.412417 -0.2930444
26 -7.412417 -0.2930444
27 -7.412417 -0.2930444
35 -7.412417 -0.2930444
36 -7.412417 -0.2930444
41 -7.412417 -0.2930444
42 -7.412417 -0.2930444
43 -7.412417 -0.2930444
44 -7.412417 -0.2930444
45 -7.412417 -0.2930444
46 -7.412417 -0.2930444
201 -7.412417 -0.2930444
202 -7.412417 -0.2930444
203 -7.412417 -0.2930444
204 -7.412417 -0.2930444
209 -7.412417 -0.2930444
210 -7.412417 -0.2930444
211 -7.412417 -0.2930444
212 -7.412417 -0.2930444
213 -7.412417 -0.2930444
214 -7.412417 -0.2930444
217 -7.412417 -0.2930444
218 -7.412417 -0.2930444
219 -7.412417 -0.2930444
220 -7.412417 -0.2930444
221 -7.412417 -0.2930444
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 -3.53698 -5.545262
4 -3.53698 -5.545262
11 -3.53698 -5.545262
12 -3.53698 -5.545262
19 -3.53698 -5.545262
20 -3.53698 -5.545262
26 -3.53698 -5.545262
27 -3.53698 -5.545262
35 -3.53698 -5.545262
36 -3.53698 -5.545262
41 -3.53698 -5.545262
42 -3.53698 -5.545262
43 -3.53698 -5.545262
44 -3.53698 -5.545262
45 -3.53698 -5.545262
46 -3.53698 -5.545262
201 -3.53698 -5.545262
202 -3.53698 -5.545262
203 -3.53698 -5.545262
204 -3.53698 -5.545262
209 -3.53698 -5.545262
210 -3.53698 -5.545262
211 -3.53698 -5.545262
212 -3.53698 -5.545262
213 -3.53698 -5.545262
214 -3.53698 -5.545262
217 -3.53698 -5.545262
218 -3.53698 -5.545262
219 -3.53698 -5.545262
220 -3.53698 -5.545262
221 -3.53698 -5.545262
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -6.403994 -5.597118
4 -6.403994 -5.597118
11 -6.403994 -5.597118
12 -6.403994 -5.597118
19 -6.403994 -5.597118
20 -6.403994 -5.597118
26 -6.403994 -5.597118
27 -6.403994 -5.597118
35 -6.403994 -5.597118
36 -6.403994 -5.597118
41 -6.403994 -5.597118
42 -6.403994 -5.597118
43 -6.403994 -5.597118
44 -6.403994 -5.597118
45 -6.403994 -5.597118
46 -6.403994 -5.597118
201 -6.403994 -5.597118
202 -6.403994 -5.597118
203 -6.403994 -5.597118
204 -6.403994 -5.597118
209 -6.403994 -5.597118
210 -6.403994 -5.597118
211 -6.403994 -5.597118
212 -6.403994 -5.597118
213 -6.403994 -5.597118
214 -6.403994 -5.597118
217 -6.403994 -5.597118
218 -6.403994 -5.597118
219 -6.403994 -5.597118
220 -6.403994 -5.597118
221 -6.403994 -5.597118
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chlafig<-ggplot(phys, aes(y=Chl.a_ug.cm2, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
chlafig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chla_stress_fig<-ggplot(phys_stress, aes(y=Chl.a_ug.cm2, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Chl.a_ug.cm2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Chl.a_ug.cm2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
geom_boxplot(alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
chla_stress_fig
library(Rmisc)
chla_sum<-summarySE(phys, measurevar='Chl.a_ug.cm2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
chla_sumchlafig_3<-ggplot(chla_sum, aes(y=Chl.a_ug.cm2, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=chla_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "chla", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Chl.a_ug.cm2-se, ymax=Chl.a_ug.cm2+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statchlafig_3
##Chlorphyll a per symbiont ###Normality
hist(phys$pg.Chl.a.per.zoox)
chla.lm<- lm(pg.Chl.a.per.zoox~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(chla.lm, ask=FALSE, which=1:6)
###Stats
chla.lme <- lme(pg.Chl.a.per.zoox~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(chla.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: pg.Chl.a.per.zoox
Chisq Df Pr(>Chisq)
(Intercept) 22.2620 1 2.379e-06 ***
Species 4.1785 1 0.04094 *
Bleach 2.0960 1 0.14768
Months 16.9046 7 0.01802 *
Species:Bleach 2.8932 1 0.08895 .
Species:Months 14.1502 7 0.04857 *
Bleach:Months 5.2984 7 0.62360
Species:Bleach:Months 3.7589 7 0.80709
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(chla.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 10.35 1.98 43 6.36 14.34
Porites compressa 0 22.53 2.01 42 18.48 26.58
Montipora capitata 10 5.90 2.10 43 1.67 10.13
Porites compressa 10 9.74 2.05 42 5.59 13.88
Montipora capitata 12 6.44 1.98 43 2.45 10.43
Porites compressa 12 15.21 2.11 42 10.95 19.46
Montipora capitata 17 8.39 1.98 43 4.40 12.38
Porites compressa 17 9.73 2.05 42 5.58 13.87
Montipora capitata 20 5.71 2.00 43 1.67 9.74
Porites compressa 20 8.52 2.05 42 4.39 12.65
Montipora capitata 24 5.80 2.03 43 1.71 9.90
Porites compressa 24 8.13 2.18 42 3.73 12.54
Montipora capitata 29 5.72 2.03 43 1.63 9.81
Porites compressa 29 10.71 2.11 42 6.45 14.96
Montipora capitata 35 2.45 2.39 43 -2.36 7.26
Porites compressa 35 7.13 2.28 42 2.53 11.73
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months0 - Months10 4.44364 1.88 199 2.361 0.2665
Months0 - Months12 3.91050 1.75 199 2.236 0.3347
Months0 - Months17 1.95350 1.75 199 1.117 0.9524
Months0 - Months20 4.64117 1.78 199 2.613 0.1575
Months0 - Months24 4.54365 1.81 199 2.515 0.1953
Months0 - Months29 4.62587 1.81 199 2.560 0.1770
Months0 - Months35 7.89779 2.30 199 3.439 0.0160
Months10 - Months12 -0.53314 1.88 199 -0.283 1.0000
Months10 - Months17 -2.49014 1.88 199 -1.323 0.8891
Months10 - Months20 0.19753 1.91 199 0.103 1.0000
Months10 - Months24 0.10001 1.92 199 0.052 1.0000
Months10 - Months29 0.18224 1.92 199 0.095 1.0000
Months10 - Months35 3.45415 2.39 199 1.444 0.8358
Months12 - Months17 -1.95700 1.75 199 -1.119 0.9520
Months12 - Months20 0.73067 1.78 199 0.411 0.9999
Months12 - Months24 0.63315 1.81 199 0.350 1.0000
Months12 - Months29 0.71537 1.81 199 0.396 0.9999
Months12 - Months35 3.98729 2.30 199 1.736 0.6637
Months17 - Months20 2.68767 1.78 199 1.513 0.7997
Months17 - Months24 2.59015 1.81 199 1.434 0.8406
Months17 - Months29 2.67238 1.81 199 1.479 0.8177
Months17 - Months35 5.94429 2.30 199 2.588 0.1665
Months20 - Months24 -0.09751 1.83 199 -0.053 1.0000
Months20 - Months29 -0.01529 1.83 199 -0.008 1.0000
Months20 - Months35 3.25662 2.31 199 1.408 0.8529
Months24 - Months29 0.08222 1.84 199 0.045 1.0000
Months24 - Months35 3.35414 2.33 199 1.441 0.8368
Months29 - Months35 3.27191 2.33 199 1.406 0.8537
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months0 - Months10 12.79693 1.87 199 6.861 <.0001
Months0 - Months12 7.32622 1.92 199 3.808 0.0045
Months0 - Months17 12.80630 1.87 199 6.866 <.0001
Months0 - Months20 14.00886 1.86 199 7.549 <.0001
Months0 - Months24 14.39742 2.00 199 7.182 <.0001
Months0 - Months29 11.82519 1.92 199 6.144 <.0001
Months0 - Months35 15.39971 2.19 199 7.029 <.0001
Months10 - Months12 -5.47070 1.92 199 -2.849 0.0890
Months10 - Months17 0.00937 1.85 199 0.005 1.0000
Months10 - Months20 1.21194 1.85 199 0.654 0.9980
Months10 - Months24 1.60049 2.00 199 0.800 0.9930
Months10 - Months29 -0.97173 1.92 199 -0.506 0.9996
Months10 - Months35 2.60278 2.18 199 1.191 0.9336
Months12 - Months17 5.48008 1.92 199 2.854 0.0879
Months12 - Months20 6.68264 1.91 199 3.498 0.0132
Months12 - Months24 7.07120 2.04 199 3.460 0.0150
Months12 - Months29 4.49897 1.97 199 2.289 0.3048
Months12 - Months35 8.07348 2.22 199 3.639 0.0082
Months17 - Months20 1.20256 1.85 199 0.649 0.9981
Months17 - Months24 1.59112 2.00 199 0.796 0.9932
Months17 - Months29 -0.98111 1.92 199 -0.511 0.9996
Months17 - Months35 2.59341 2.18 199 1.187 0.9348
Months20 - Months24 0.38855 1.99 199 0.195 1.0000
Months20 - Months29 -2.18367 1.91 199 -1.143 0.9464
Months20 - Months35 1.39084 2.18 199 0.639 0.9983
Months24 - Months29 -2.57222 2.03 199 -1.266 0.9104
Months24 - Months35 1.00229 2.30 199 0.436 0.9999
Months29 - Months35 3.57451 2.22 199 1.611 0.7429
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 8 estimates ###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chlafig2<-ggplot(phys, aes(y=pg.Chl.a.per.zoox, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})), limits=c(0,50))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
chlafig2
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chla_stress_fig2<-ggplot(phys_stress, aes(y=pg.Chl.a.per.zoox, x=Months, color=Bleach, fill=Bleach))+
#geom_point(alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
geom_boxplot(alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})), limits=c(0,50))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
chla_stress_fig2
library(Rmisc)
chlacell_sum<-summarySE(phys, measurevar='pg.Chl.a.per.zoox', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
chlacell_sumchlacellfig_3<-ggplot(chlacell_sum, aes(y=pg.Chl.a.per.zoox, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=chlacell_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "chlacell", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=pg.Chl.a.per.zoox-se, ymax=pg.Chl.a.per.zoox+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statchlacellfig_3
##Melanin
###Normality
hist(phys$Melanin_per_tissue)
mel.lm<- lm(Melanin_per_tissue~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(mel.lm, ask=FALSE, which=1:6)
###Stats
mel.lme <- lme(Melanin_per_tissue~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(mel.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, SpeciesPorites compressa:Months10, BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months10Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Melanin_per_tissue
Chisq Df Pr(>Chisq)
(Intercept) 18.5389 1 1.665e-05 ***
Species 9.0151 1 0.002678 **
Bleach 0.4796 1 0.488592
Months 5.6176 6 0.467357
Species:Bleach 0.0130 1 0.909084
Species:Months 17.0708 6 0.009027 **
Bleach:Months 1.7906 6 0.937914
Species:Bleach:Months 5.7355 6 0.453467
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(mel.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 10 0.000717 0.000125 41 0.000464 0.000970
Porites compressa 10 0.001466 0.000119 40 0.001225 0.001706
Montipora capitata 12 0.000646 0.000112 41 0.000419 0.000873
Porites compressa 12 0.001706 0.000118 40 0.001467 0.001945
Montipora capitata 17 0.000813 0.000112 41 0.000586 0.001040
Porites compressa 17 0.002319 0.000119 40 0.002079 0.002560
Montipora capitata 20 0.000969 0.000115 41 0.000737 0.001201
Porites compressa 20 0.002547 0.000118 40 0.002308 0.002786
Montipora capitata 24 0.000887 0.000118 41 0.000649 0.001125
Porites compressa 24 0.002197 0.000133 40 0.001929 0.002465
Montipora capitata 29 0.000957 0.000118 41 0.000719 0.001195
Porites compressa 29 0.001828 0.000125 40 0.001575 0.002080
Montipora capitata 35 0.000670 0.000153 41 0.000361 0.000980
Porites compressa 35 0.001399 0.000163 40 0.001069 0.001729
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months10 - Months12 7.12e-05 0.000152 165 0.469 0.9992
Months10 - Months17 -9.60e-05 0.000152 165 -0.632 0.9957
Months10 - Months20 -2.52e-04 0.000154 165 -1.635 0.6602
Months10 - Months24 -1.70e-04 0.000155 165 -1.096 0.9286
Months10 - Months29 -2.40e-04 0.000155 165 -1.550 0.7140
Months10 - Months35 4.67e-05 0.000186 165 0.251 1.0000
Months12 - Months17 -1.67e-04 0.000142 165 -1.182 0.9001
Months12 - Months20 -3.23e-04 0.000144 165 -2.249 0.2755
Months12 - Months24 -2.41e-04 0.000146 165 -1.651 0.6491
Months12 - Months29 -3.11e-04 0.000146 165 -2.134 0.3379
Months12 - Months35 -2.46e-05 0.000178 165 -0.138 1.0000
Months17 - Months20 -1.56e-04 0.000144 165 -1.085 0.9317
Months17 - Months24 -7.38e-05 0.000146 165 -0.506 0.9988
Months17 - Months29 -1.44e-04 0.000146 165 -0.988 0.9560
Months17 - Months35 1.43e-04 0.000178 165 0.801 0.9846
Months20 - Months24 8.21e-05 0.000148 165 0.554 0.9979
Months20 - Months29 1.17e-05 0.000148 165 0.079 1.0000
Months20 - Months35 2.99e-04 0.000180 165 1.662 0.6420
Months24 - Months29 -7.04e-05 0.000149 165 -0.472 0.9992
Months24 - Months35 2.16e-04 0.000181 165 1.196 0.8947
Months29 - Months35 2.87e-04 0.000181 165 1.585 0.6919
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months10 - Months12 -2.40e-04 0.000150 165 -1.605 0.6794
Months10 - Months17 -8.54e-04 0.000150 165 -5.688 <.0001
Months10 - Months20 -1.08e-03 0.000150 165 -7.222 <.0001
Months10 - Months24 -7.31e-04 0.000161 165 -4.537 0.0002
Months10 - Months29 -3.62e-04 0.000155 165 -2.337 0.2331
Months10 - Months35 6.68e-05 0.000190 165 0.351 0.9998
Months12 - Months17 -6.13e-04 0.000150 165 -4.097 0.0013
Months12 - Months20 -8.41e-04 0.000149 165 -5.638 <.0001
Months12 - Months24 -4.91e-04 0.000161 165 -3.057 0.0409
Months12 - Months29 -1.22e-04 0.000154 165 -0.788 0.9858
Months12 - Months35 3.07e-04 0.000190 165 1.620 0.6698
Months17 - Months20 -2.27e-04 0.000150 165 -1.519 0.7328
Months17 - Months24 1.23e-04 0.000161 165 0.760 0.9883
Months17 - Months29 4.92e-04 0.000155 165 3.175 0.0290
Months17 - Months35 9.21e-04 0.000190 165 4.841 0.0001
Months20 - Months24 3.50e-04 0.000161 165 2.179 0.3124
Months20 - Months29 7.19e-04 0.000154 165 4.661 0.0001
Months20 - Months35 1.15e-03 0.000190 165 6.055 <.0001
Months24 - Months29 3.69e-04 0.000164 165 2.247 0.2765
Months24 - Months35 7.98e-04 0.000199 165 4.010 0.0018
Months29 - Months35 4.29e-04 0.000193 165 2.222 0.2894
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 7 estimates summary(mel.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.0002300293 0.0004474928
Fixed effects: Melanin_per_tissue ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M12 SPc:M17
SpeciesPorites compressa -0.730
BleachNon-bleach -0.746 0.544
Months12 -0.712 0.520 0.531
Months17 -0.712 0.520 0.531 0.597
Months20 -0.697 0.508 0.520 0.583 0.583
Months24 -0.692 0.505 0.516 0.579 0.579 0.566
Months29 -0.692 0.505 0.516 0.579 0.579 0.566 0.568
Months35 -0.563 0.411 0.420 0.454 0.454 0.447 0.445 0.445
SpeciesPorites compressa:BleachNon-bleach 0.547 -0.741 -0.733 -0.389 -0.389 -0.381 -0.378 -0.378 -0.308
SpeciesPorites compressa:Months12 0.509 -0.690 -0.380 -0.715 -0.426 -0.417 -0.414 -0.414 -0.325 0.520
SpeciesPorites compressa:Months17 0.503 -0.677 -0.375 -0.421 -0.706 -0.412 -0.409 -0.409 -0.321 0.507 0.555
SpeciesPorites compressa:Months20 0.504 -0.682 -0.376 -0.422 -0.422 -0.724 -0.409 -0.409 -0.324 0.514 0.559 0.549
SpeciesPorites compressa:Months24 0.479 -0.662 -0.358 -0.401 -0.401 -0.392 -0.693 -0.394 -0.308 0.504 0.537 0.525
SpeciesPorites compressa:Months29 0.489 -0.673 -0.365 -0.410 -0.410 -0.400 -0.402 -0.707 -0.314 0.511 0.547 0.536
SpeciesPorites compressa:Months35 0.416 -0.570 -0.311 -0.336 -0.336 -0.330 -0.329 -0.329 -0.739 0.425 0.444 0.437
BleachNon-bleach:Months12 0.523 -0.381 -0.687 -0.734 -0.438 -0.428 -0.425 -0.425 -0.333 0.503 0.524 0.309
BleachNon-bleach:Months17 0.523 -0.381 -0.687 -0.438 -0.734 -0.428 -0.425 -0.425 -0.333 0.503 0.313 0.518
BleachNon-bleach:Months20 0.517 -0.378 -0.679 -0.433 -0.433 -0.743 -0.420 -0.420 -0.332 0.497 0.310 0.306
BleachNon-bleach:Months24 0.507 -0.370 -0.665 -0.424 -0.424 -0.414 -0.733 -0.416 -0.326 0.487 0.303 0.299
BleachNon-bleach:Months29 0.507 -0.370 -0.665 -0.424 -0.424 -0.414 -0.416 -0.733 -0.326 0.487 0.303 0.299
BleachNon-bleach:Months35 0.443 -0.324 -0.577 -0.358 -0.358 -0.352 -0.350 -0.350 -0.787 0.423 0.256 0.252
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.371 0.502 0.488 0.521 0.311 0.304 0.302 0.302 0.237 -0.669 -0.731 -0.405
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.372 0.500 0.489 0.311 0.522 0.304 0.302 0.302 0.237 -0.667 -0.410 -0.739
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.370 0.499 0.486 0.310 0.310 0.531 0.301 0.301 0.238 -0.665 -0.412 -0.403
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.348 0.483 0.456 0.291 0.291 0.284 0.503 0.286 0.223 -0.644 -0.391 -0.381
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.355 0.492 0.466 0.297 0.297 0.290 0.292 0.513 0.228 -0.655 -0.399 -0.389
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.310 0.424 0.404 0.250 0.250 0.246 0.245 0.245 0.551 -0.552 -0.332 -0.326
SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M12 BN-:M17 BN-:M20 BN-:M24 BN-:M29 BN-:M3 SPc:BN-:M12
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24 0.530
SpeciesPorites compressa:Months29 0.540 0.532
SpeciesPorites compressa:Months35 0.440 0.425 0.436
BleachNon-bleach:Months12 0.310 0.295 0.300 0.246
BleachNon-bleach:Months17 0.310 0.295 0.300 0.246 0.566
BleachNon-bleach:Months20 0.538 0.291 0.297 0.245 0.559 0.559
BleachNon-bleach:Months24 0.300 0.508 0.294 0.241 0.548 0.548 0.541
BleachNon-bleach:Months29 0.300 0.289 0.518 0.241 0.548 0.548 0.541 0.537
BleachNon-bleach:Months35 0.255 0.243 0.248 0.582 0.459 0.459 0.456 0.449 0.449
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.409 -0.393 -0.400 -0.323 -0.710 -0.402 -0.397 -0.389 -0.389 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.406 -0.388 -0.396 -0.323 -0.403 -0.711 -0.398 -0.390 -0.390 -0.327 0.533
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.736 -0.391 -0.398 -0.323 -0.400 -0.400 -0.716 -0.387 -0.387 -0.326 0.534
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.386 -0.732 -0.392 -0.310 -0.376 -0.376 -0.371 -0.686 -0.368 -0.308 0.506
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.394 -0.393 -0.732 -0.318 -0.384 -0.384 -0.379 -0.376 -0.701 -0.315 0.517
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.329 -0.315 -0.324 -0.745 -0.321 -0.321 -0.319 -0.314 -0.314 -0.700 0.429
SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months12
SpeciesPorites compressa:BleachNon-bleach:Months17
SpeciesPorites compressa:BleachNon-bleach:Months20 0.529
SpeciesPorites compressa:BleachNon-bleach:Months24 0.501 0.503
SpeciesPorites compressa:BleachNon-bleach:Months29 0.511 0.513 0.507
SpeciesPorites compressa:BleachNon-bleach:Months35 0.427 0.427 0.405 0.417
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.20574291 -0.50926467 -0.07428264 0.39904822 4.72554035
Number of Observations: 233
Number of Groups: 42 r.squaredGLMM(mel.lme) R2m R2c
[1,] 0.6242873 0.7028147####Coefficients
coef(mel.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months12 Months17 Months20 Months24 Months29 Months35
3 0.0008258971 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
4 0.0007939080 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
11 0.0007616610 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
12 0.0005896463 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
19 0.0007032111 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
20 0.0008991910 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
26 0.0007162773 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
27 0.0007588490 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
41 0.0006593915 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
42 0.0009202546 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
43 0.0007507726 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
44 0.0007973578 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
45 0.0010446768 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
46 0.0009321575 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
201 0.0005849470 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
202 0.0006344938 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
203 0.0008356053 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
204 0.0007648299 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
209 0.0010458169 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
210 0.0008728792 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
211 0.0009659106 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
212 0.0011314226 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
213 0.0007586591 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
214 0.0007833919 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
217 0.0007741247 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
218 0.0008938928 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
219 0.0007399144 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
220 0.0006482155 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
221 0.0008448906 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
222 0.0008287670 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
225 0.0008120613 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
229 0.0006690720 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
230 0.0005217918 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
235 0.0007952385 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
237 0.0012848791 0.0007681457 -0.0001732806 -0.0001415939 -5.112376e-05 0.0001450065 0.0001427679 0.0002470998 -0.0001475465
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months12 SpeciesPorites compressa:Months17
3 -3.899635e-05 0.0003004048 0.001073006
4 -3.899635e-05 0.0003004048 0.001073006
11 -3.899635e-05 0.0003004048 0.001073006
12 -3.899635e-05 0.0003004048 0.001073006
19 -3.899635e-05 0.0003004048 0.001073006
20 -3.899635e-05 0.0003004048 0.001073006
26 -3.899635e-05 0.0003004048 0.001073006
27 -3.899635e-05 0.0003004048 0.001073006
41 -3.899635e-05 0.0003004048 0.001073006
42 -3.899635e-05 0.0003004048 0.001073006
43 -3.899635e-05 0.0003004048 0.001073006
44 -3.899635e-05 0.0003004048 0.001073006
45 -3.899635e-05 0.0003004048 0.001073006
46 -3.899635e-05 0.0003004048 0.001073006
201 -3.899635e-05 0.0003004048 0.001073006
202 -3.899635e-05 0.0003004048 0.001073006
203 -3.899635e-05 0.0003004048 0.001073006
204 -3.899635e-05 0.0003004048 0.001073006
209 -3.899635e-05 0.0003004048 0.001073006
210 -3.899635e-05 0.0003004048 0.001073006
211 -3.899635e-05 0.0003004048 0.001073006
212 -3.899635e-05 0.0003004048 0.001073006
213 -3.899635e-05 0.0003004048 0.001073006
214 -3.899635e-05 0.0003004048 0.001073006
217 -3.899635e-05 0.0003004048 0.001073006
218 -3.899635e-05 0.0003004048 0.001073006
219 -3.899635e-05 0.0003004048 0.001073006
220 -3.899635e-05 0.0003004048 0.001073006
221 -3.899635e-05 0.0003004048 0.001073006
222 -3.899635e-05 0.0003004048 0.001073006
225 -3.899635e-05 0.0003004048 0.001073006
229 -3.899635e-05 0.0003004048 0.001073006
230 -3.899635e-05 0.0003004048 0.001073006
235 -3.899635e-05 0.0003004048 0.001073006
237 -3.899635e-05 0.0003004048 0.001073006
SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35
3 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
4 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
11 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
12 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
19 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
20 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
26 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
27 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
41 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
42 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
43 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
44 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
45 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
46 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
201 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
202 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
203 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
204 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
209 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
210 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
211 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
212 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
213 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
214 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
217 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
218 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
219 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
220 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
221 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
222 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
225 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
229 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
230 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
235 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
237 0.0006989138 0.0004838388 0.0002220951 2.082411e-05
BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20 BleachNon-bleach:Months24 BleachNon-bleach:Months29
3 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
4 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
11 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
12 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
19 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
20 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
26 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
27 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
41 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
42 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
43 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
44 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
45 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
46 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
201 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
202 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
203 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
204 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
209 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
210 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
211 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
212 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
213 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
214 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
217 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
218 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
219 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
220 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
221 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
222 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
225 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
229 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
230 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
235 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
237 0.0001407154 0.0002942308 0.0002138164 5.405067e-05 -1.380622e-05
BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 0.0002017695 2.222058e-05 -0.0006305275
4 0.0002017695 2.222058e-05 -0.0006305275
11 0.0002017695 2.222058e-05 -0.0006305275
12 0.0002017695 2.222058e-05 -0.0006305275
19 0.0002017695 2.222058e-05 -0.0006305275
20 0.0002017695 2.222058e-05 -0.0006305275
26 0.0002017695 2.222058e-05 -0.0006305275
27 0.0002017695 2.222058e-05 -0.0006305275
41 0.0002017695 2.222058e-05 -0.0006305275
42 0.0002017695 2.222058e-05 -0.0006305275
43 0.0002017695 2.222058e-05 -0.0006305275
44 0.0002017695 2.222058e-05 -0.0006305275
45 0.0002017695 2.222058e-05 -0.0006305275
46 0.0002017695 2.222058e-05 -0.0006305275
201 0.0002017695 2.222058e-05 -0.0006305275
202 0.0002017695 2.222058e-05 -0.0006305275
203 0.0002017695 2.222058e-05 -0.0006305275
204 0.0002017695 2.222058e-05 -0.0006305275
209 0.0002017695 2.222058e-05 -0.0006305275
210 0.0002017695 2.222058e-05 -0.0006305275
211 0.0002017695 2.222058e-05 -0.0006305275
212 0.0002017695 2.222058e-05 -0.0006305275
213 0.0002017695 2.222058e-05 -0.0006305275
214 0.0002017695 2.222058e-05 -0.0006305275
217 0.0002017695 2.222058e-05 -0.0006305275
218 0.0002017695 2.222058e-05 -0.0006305275
219 0.0002017695 2.222058e-05 -0.0006305275
220 0.0002017695 2.222058e-05 -0.0006305275
221 0.0002017695 2.222058e-05 -0.0006305275
222 0.0002017695 2.222058e-05 -0.0006305275
225 0.0002017695 2.222058e-05 -0.0006305275
229 0.0002017695 2.222058e-05 -0.0006305275
230 0.0002017695 2.222058e-05 -0.0006305275
235 0.0002017695 2.222058e-05 -0.0006305275
237 0.0002017695 2.222058e-05 -0.0006305275
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 0.0002608015 0.0001551324
4 0.0002608015 0.0001551324
11 0.0002608015 0.0001551324
12 0.0002608015 0.0001551324
19 0.0002608015 0.0001551324
20 0.0002608015 0.0001551324
26 0.0002608015 0.0001551324
27 0.0002608015 0.0001551324
41 0.0002608015 0.0001551324
42 0.0002608015 0.0001551324
43 0.0002608015 0.0001551324
44 0.0002608015 0.0001551324
45 0.0002608015 0.0001551324
46 0.0002608015 0.0001551324
201 0.0002608015 0.0001551324
202 0.0002608015 0.0001551324
203 0.0002608015 0.0001551324
204 0.0002608015 0.0001551324
209 0.0002608015 0.0001551324
210 0.0002608015 0.0001551324
211 0.0002608015 0.0001551324
212 0.0002608015 0.0001551324
213 0.0002608015 0.0001551324
214 0.0002608015 0.0001551324
217 0.0002608015 0.0001551324
218 0.0002608015 0.0001551324
219 0.0002608015 0.0001551324
220 0.0002608015 0.0001551324
221 0.0002608015 0.0001551324
222 0.0002608015 0.0001551324
225 0.0002608015 0.0001551324
229 0.0002608015 0.0001551324
230 0.0002608015 0.0001551324
235 0.0002608015 0.0001551324
237 0.0002608015 0.0001551324
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.0002007325 -8.194412e-05
4 -0.0002007325 -8.194412e-05
11 -0.0002007325 -8.194412e-05
12 -0.0002007325 -8.194412e-05
19 -0.0002007325 -8.194412e-05
20 -0.0002007325 -8.194412e-05
26 -0.0002007325 -8.194412e-05
27 -0.0002007325 -8.194412e-05
41 -0.0002007325 -8.194412e-05
42 -0.0002007325 -8.194412e-05
43 -0.0002007325 -8.194412e-05
44 -0.0002007325 -8.194412e-05
45 -0.0002007325 -8.194412e-05
46 -0.0002007325 -8.194412e-05
201 -0.0002007325 -8.194412e-05
202 -0.0002007325 -8.194412e-05
203 -0.0002007325 -8.194412e-05
204 -0.0002007325 -8.194412e-05
209 -0.0002007325 -8.194412e-05
210 -0.0002007325 -8.194412e-05
211 -0.0002007325 -8.194412e-05
212 -0.0002007325 -8.194412e-05
213 -0.0002007325 -8.194412e-05
214 -0.0002007325 -8.194412e-05
217 -0.0002007325 -8.194412e-05
218 -0.0002007325 -8.194412e-05
219 -0.0002007325 -8.194412e-05
220 -0.0002007325 -8.194412e-05
221 -0.0002007325 -8.194412e-05
222 -0.0002007325 -8.194412e-05
225 -0.0002007325 -8.194412e-05
229 -0.0002007325 -8.194412e-05
230 -0.0002007325 -8.194412e-05
235 -0.0002007325 -8.194412e-05
237 -0.0002007325 -8.194412e-05
[ reached 'max' / getOption("max.print") -- omitted 7 rows ]###Figure
#mel$Date<- as.Date(as.POSIXct(mel$Date, origin="1970-01-01"))
melfig<-ggplot(phys, aes(y=Melanin_per_tissue, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Melanin~(mg~melanin~'\U2219'~mg~tissue^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
melfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
mel_stress_fig<-ggplot(phys_stress, aes(y=Melanin_per_tissue, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Melanin_per_tissue, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Melanin_per_tissue, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
geom_boxplot(alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Melanin~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
mel_stress_fig
library(Rmisc)
mel_sum<-summarySE(phys, measurevar='Melanin_per_tissue', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedmel_summelfig_3<-ggplot(mel_sum, aes(y=Melanin_per_tissue, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=mel_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "mel", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Melanin_per_tissue-se, ymax=Melanin_per_tissue+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Melanin~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(0,0.003))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statmelfig_3
##PPO
ppo<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/PPO all R.csv", strip.white=T)
ppo$Date<- as.Date(ppo$Date, format = "%Y-%m-%d")
ppo$Bleach<-as.factor(ppo$Bleach)
#ppo$Months<-as.factor(ppo$Months)
ppo$Species<-as.factor(ppo$Species)
ppo$Coral_ID<-as.factor(ppo$Coral_ID)
ppo###Normality
hist(phys$PPO)
ppo.lm<- lm(PPO~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(ppo.lm, ask=FALSE, which=1:6)
###Stats
ppo.lme <- lme(PPO~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(ppo.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, SpeciesPorites compressa:Months10, BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months10Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: PPO
Chisq Df Pr(>Chisq)
(Intercept) 2.8579 1 0.090928 .
Species 0.1019 1 0.749573
Bleach 0.1714 1 0.678897
Months 44.6291 6 5.545e-08 ***
Species:Bleach 0.0649 1 0.798951
Species:Months 4.7662 6 0.574124
Bleach:Months 7.4601 6 0.280387
Species:Bleach:Months 18.2230 6 0.005698 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(ppo.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Months")
tukey3$`emmeans of Species, Bleach, Months`
Species Bleach Months emmean SE df lower.CL upper.CL
Montipora capitata Bleach 10 0.166 0.0982 41 -0.03231 0.364
Porites compressa Bleach 10 0.123 0.0919 40 -0.06278 0.309
Montipora capitata Non-bleach 10 0.112 0.0869 41 -0.06379 0.287
Porites compressa Non-bleach 10 0.115 0.0824 40 -0.05188 0.281
Montipora capitata Bleach 12 0.588 0.0825 41 0.42092 0.754
Porites compressa Bleach 12 0.590 0.0868 40 0.41449 0.765
Montipora capitata Non-bleach 12 0.576 0.0825 41 0.40958 0.743
Porites compressa Non-bleach 12 1.040 0.0868 40 0.86449 1.215
Montipora capitata Bleach 17 0.897 0.0825 41 0.73075 1.064
Porites compressa Bleach 17 1.010 0.0919 40 0.82446 1.196
Montipora capitata Non-bleach 17 1.151 0.0825 41 0.98457 1.318
Porites compressa Non-bleach 17 0.970 0.0824 40 0.80357 1.136
Montipora capitata Bleach 20 0.577 0.0869 41 0.40118 0.752
Porites compressa Bleach 20 0.742 0.0868 40 0.56672 0.917
Montipora capitata Non-bleach 20 0.456 0.0825 41 0.28959 0.623
Porites compressa Non-bleach 20 0.607 0.0868 40 0.43120 0.782
Montipora capitata Bleach 24 0.577 0.0869 41 0.40123 0.752
Porites compressa Bleach 24 0.737 0.0979 40 0.53885 0.935
Montipora capitata Non-bleach 24 0.481 0.0869 41 0.30567 0.657
Porites compressa Non-bleach 24 0.926 0.0980 40 0.72848 1.125
Montipora capitata Bleach 29 0.562 0.0869 41 0.38643 0.737
Porites compressa Bleach 29 0.834 0.0917 40 0.64894 1.020
Montipora capitata Non-bleach 29 0.625 0.0869 41 0.44931 0.800
Porites compressa Non-bleach 29 0.551 0.0918 40 0.36549 0.737
Montipora capitata Bleach 35 0.185 0.1293 41 -0.07588 0.446
Porites compressa Bleach 35 0.205 0.0981 40 0.00697 0.404
Montipora capitata Non-bleach 35 0.178 0.0981 41 -0.02017 0.376
Porites compressa Non-bleach 35 0.166 0.1156 40 -0.06745 0.400
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Bleach, Months | Species, Bleach`
Species = Montipora capitata, Bleach = Bleach:
3 estimate SE df t.ratio p.value
Months10 - Months12 -0.421642 0.123 168 -3.428 0.0132
Months10 - Months17 -0.731469 0.123 168 -5.947 <.0001
Months10 - Months20 -0.410614 0.126 168 -3.256 0.0227
Months10 - Months24 -0.410757 0.126 168 -3.272 0.0216
Months10 - Months29 -0.395955 0.126 168 -3.154 0.0308
Months10 - Months35 -0.019251 0.159 168 -0.121 1.0000
Months12 - Months17 -0.309828 0.111 168 -2.793 0.0830
Months12 - Months20 0.011028 0.114 168 0.097 1.0000
Months12 - Months24 0.010885 0.114 168 0.095 1.0000
Months12 - Months29 0.025687 0.114 168 0.225 1.0000
Months12 - Months35 0.402391 0.150 168 2.681 0.1095
Months17 - Months20 0.320855 0.114 168 2.810 0.0794
Months17 - Months24 0.320713 0.114 168 2.808 0.0799
Months17 - Months29 0.335515 0.114 168 2.938 0.0568
Months17 - Months35 0.712218 0.150 168 4.746 0.0001
Months20 - Months24 -0.000143 0.117 168 -0.001 1.0000
Months20 - Months29 0.014659 0.117 168 0.125 1.0000
Months20 - Months35 0.391363 0.152 168 2.570 0.1419
Months24 - Months29 0.014802 0.117 168 0.127 1.0000
Months24 - Months35 0.391506 0.152 168 2.572 0.1415
Months29 - Months35 0.376704 0.152 168 2.474 0.1754
Species = Porites compressa, Bleach = Bleach:
3 estimate SE df t.ratio p.value
Months10 - Months12 -0.466785 0.121 168 -3.866 0.0030
Months10 - Months17 -0.887241 0.124 168 -7.155 <.0001
Months10 - Months20 -0.619013 0.121 168 -5.126 <.0001
Months10 - Months24 -0.613632 0.130 168 -4.725 0.0001
Months10 - Months29 -0.711312 0.125 168 -5.685 <.0001
Months10 - Months35 -0.082206 0.130 168 -0.631 0.9957
Months12 - Months17 -0.420456 0.121 168 -3.482 0.0111
Months12 - Months20 -0.152228 0.117 168 -1.302 0.8502
Months12 - Months24 -0.146846 0.126 168 -1.165 0.9063
Months12 - Months29 -0.244527 0.121 168 -2.016 0.4083
Months12 - Months35 0.384580 0.127 168 3.029 0.0442
Months17 - Months20 0.268228 0.121 168 2.221 0.2898
Months17 - Months24 0.273610 0.130 168 2.107 0.3535
Months17 - Months29 0.175929 0.125 168 1.406 0.7979
Months17 - Months35 0.805036 0.130 168 6.183 <.0001
Months20 - Months24 0.005382 0.126 168 0.043 1.0000
Months20 - Months29 -0.092299 0.121 168 -0.761 0.9882
Months20 - Months35 0.536808 0.127 168 4.228 0.0008
Months24 - Months29 -0.097681 0.129 168 -0.759 0.9884
Months24 - Months35 0.531426 0.135 168 3.941 0.0022
Months29 - Months35 0.629106 0.130 168 4.833 0.0001
Species = Montipora capitata, Bleach = Non-bleach:
3 estimate SE df t.ratio p.value
Months10 - Months12 -0.464571 0.114 168 -4.068 0.0014
Months10 - Months17 -1.039566 0.114 168 -9.103 <.0001
Months10 - Months20 -0.344584 0.114 168 -3.017 0.0456
Months10 - Months24 -0.369459 0.117 168 -3.160 0.0303
Months10 - Months29 -0.513107 0.117 168 -4.389 0.0004
Months10 - Months35 -0.066200 0.126 168 -0.525 0.9985
Months12 - Months17 -0.574996 0.111 168 -5.184 <.0001
Months12 - Months20 0.119987 0.111 168 1.082 0.9327
Months12 - Months24 0.095112 0.114 168 0.833 0.9812
Months12 - Months29 -0.048536 0.114 168 -0.425 0.9995
Months12 - Months35 0.398370 0.124 168 3.222 0.0252
Months17 - Months20 0.694983 0.111 168 6.266 <.0001
Months17 - Months24 0.670108 0.114 168 5.868 <.0001
Months17 - Months29 0.526459 0.114 168 4.610 0.0002
Months17 - Months35 0.973366 0.124 168 7.873 <.0001
Months20 - Months24 -0.024875 0.114 168 -0.218 1.0000
Months20 - Months29 -0.168523 0.114 168 -1.476 0.7589
Months20 - Months35 0.278383 0.124 168 2.252 0.2741
Months24 - Months29 -0.143648 0.117 168 -1.229 0.8821
Months24 - Months35 0.303258 0.126 168 2.403 0.2039
Months29 - Months35 0.446907 0.126 168 3.541 0.0091
Species = Porites compressa, Bleach = Non-bleach:
3 estimate SE df t.ratio p.value
Months10 - Months12 -0.925390 0.114 168 -8.106 <.0001
Months10 - Months17 -0.855443 0.111 168 -7.713 <.0001
Months10 - Months20 -0.492104 0.114 168 -4.310 0.0005
Months10 - Months24 -0.811917 0.123 168 -6.576 <.0001
Months10 - Months29 -0.436494 0.119 168 -3.682 0.0057
Months10 - Months35 -0.051600 0.137 168 -0.376 0.9998
Months12 - Months17 0.069948 0.114 168 0.613 0.9963
Months12 - Months20 0.433287 0.117 168 3.706 0.0052
Months12 - Months24 0.113473 0.126 168 0.900 0.9721
Months12 - Months29 0.488896 0.121 168 4.032 0.0016
Months12 - Months35 0.873790 0.140 168 6.256 <.0001
Months17 - Months20 0.363339 0.114 168 3.183 0.0283
Months17 - Months24 0.043525 0.123 168 0.353 0.9998
Months17 - Months29 0.418949 0.119 168 3.534 0.0094
Months17 - Months35 0.803843 0.137 168 5.852 <.0001
Months20 - Months24 -0.319813 0.126 168 -2.537 0.1531
Months20 - Months29 0.055610 0.121 168 0.459 0.9993
Months20 - Months35 0.440504 0.140 168 3.154 0.0308
Months24 - Months29 0.375423 0.129 168 2.918 0.0599
Months24 - Months35 0.760317 0.148 168 5.149 <.0001
Months29 - Months35 0.384894 0.143 168 2.688 0.1078
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 7 estimates summary(ppo.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.08171943 0.2480159
Fixed effects: PPO ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M12 SPc:M17
SpeciesPorites compressa -0.730
BleachNon-bleach -0.749 0.547
Months12 -0.743 0.543 0.557
Months17 -0.743 0.543 0.557 0.593
Months20 -0.727 0.531 0.544 0.580 0.580
Months24 -0.724 0.528 0.542 0.578 0.578 0.565
Months29 -0.724 0.528 0.542 0.578 0.578 0.565 0.566
Months35 -0.585 0.427 0.438 0.459 0.459 0.450 0.449 0.449
SpeciesPorites compressa:BleachNon-bleach 0.546 -0.746 -0.729 -0.406 -0.406 -0.397 -0.395 -0.395 -0.319
SpeciesPorites compressa:Months12 0.530 -0.722 -0.397 -0.714 -0.423 -0.414 -0.412 -0.412 -0.327 0.542
SpeciesPorites compressa:Months17 0.523 -0.709 -0.392 -0.418 -0.704 -0.409 -0.407 -0.407 -0.323 0.531 0.554
SpeciesPorites compressa:Months20 0.525 -0.713 -0.393 -0.419 -0.419 -0.722 -0.408 -0.408 -0.325 0.535 0.556 0.547
SpeciesPorites compressa:Months24 0.503 -0.691 -0.377 -0.402 -0.402 -0.392 -0.695 -0.393 -0.312 0.521 0.536 0.527
SpeciesPorites compressa:Months29 0.513 -0.703 -0.384 -0.409 -0.409 -0.400 -0.401 -0.708 -0.318 0.530 0.546 0.537
SpeciesPorites compressa:Months35 0.453 -0.616 -0.339 -0.355 -0.355 -0.349 -0.348 -0.348 -0.774 0.460 0.471 0.464
BleachNon-bleach:Months12 0.545 -0.398 -0.721 -0.733 -0.435 -0.425 -0.423 -0.423 -0.336 0.526 0.523 0.306
BleachNon-bleach:Months17 0.545 -0.398 -0.721 -0.435 -0.733 -0.425 -0.423 -0.423 -0.336 0.526 0.310 0.516
BleachNon-bleach:Months20 0.539 -0.393 -0.712 -0.430 -0.430 -0.741 -0.418 -0.418 -0.334 0.519 0.307 0.303
BleachNon-bleach:Months24 0.530 -0.387 -0.701 -0.423 -0.423 -0.413 -0.732 -0.414 -0.328 0.511 0.302 0.298
BleachNon-bleach:Months29 0.530 -0.387 -0.701 -0.423 -0.423 -0.413 -0.414 -0.732 -0.328 0.511 0.302 0.298
BleachNon-bleach:Months35 0.458 -0.335 -0.603 -0.360 -0.360 -0.353 -0.352 -0.352 -0.784 0.440 0.257 0.253
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.387 0.526 0.512 0.520 0.309 0.302 0.301 0.301 0.239 -0.701 -0.730 -0.404
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.387 0.524 0.512 0.309 0.520 0.302 0.301 0.301 0.239 -0.699 -0.409 -0.739
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.385 0.523 0.509 0.307 0.307 0.530 0.299 0.299 0.239 -0.697 -0.409 -0.401
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.365 0.504 0.483 0.291 0.291 0.285 0.504 0.286 0.226 -0.672 -0.391 -0.382
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.373 0.513 0.493 0.297 0.297 0.291 0.291 0.515 0.231 -0.684 -0.398 -0.390
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.335 0.456 0.442 0.263 0.263 0.258 0.257 0.257 0.574 -0.603 -0.350 -0.344
SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M12 BN-:M17 BN-:M20 BN-:M24 BN-:M29 BN-:M3 SPc:BN-:M12
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24 0.530
SpeciesPorites compressa:Months29 0.540 0.528
SpeciesPorites compressa:Months35 0.466 0.452 0.461
BleachNon-bleach:Months12 0.307 0.294 0.300 0.260
BleachNon-bleach:Months17 0.307 0.294 0.300 0.260 0.563
BleachNon-bleach:Months20 0.535 0.291 0.296 0.258 0.556 0.556
BleachNon-bleach:Months24 0.298 0.509 0.293 0.254 0.547 0.547 0.540
BleachNon-bleach:Months29 0.298 0.288 0.518 0.254 0.547 0.547 0.540 0.535
BleachNon-bleach:Months35 0.255 0.244 0.249 0.607 0.464 0.464 0.460 0.453 0.453
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.407 -0.392 -0.399 -0.343 -0.710 -0.400 -0.395 -0.389 -0.389 -0.330
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.404 -0.389 -0.397 -0.343 -0.400 -0.710 -0.395 -0.389 -0.389 -0.330 0.532
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.735 -0.390 -0.397 -0.342 -0.398 -0.398 -0.715 -0.386 -0.386 -0.328 0.532
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.386 -0.730 -0.387 -0.330 -0.377 -0.377 -0.372 -0.689 -0.369 -0.313 0.507
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.394 -0.388 -0.731 -0.336 -0.385 -0.385 -0.380 -0.377 -0.703 -0.319 0.517
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.346 -0.335 -0.341 -0.741 -0.340 -0.340 -0.336 -0.332 -0.332 -0.732 0.454
SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months12
SpeciesPorites compressa:BleachNon-bleach:Months17
SpeciesPorites compressa:BleachNon-bleach:Months20 0.529
SpeciesPorites compressa:BleachNon-bleach:Months24 0.503 0.504
SpeciesPorites compressa:BleachNon-bleach:Months29 0.513 0.514 0.502
SpeciesPorites compressa:BleachNon-bleach:Months35 0.452 0.451 0.432 0.442
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.23210616 -0.49095801 -0.03706976 0.36723306 5.78496414
Number of Observations: 236
Number of Groups: 42 r.squaredGLMM(ppo.lme) R2m R2c
[1,] 0.576574 0.6180415####Coefficients
coef(ppo.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months12 Months17 Months20 Months24 Months29 Months35
3 0.21003463 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
4 0.16565610 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
11 0.25416927 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
12 0.16387851 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
19 0.13353225 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
20 0.15023763 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
26 0.08390408 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
27 0.13863682 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
41 0.13286505 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
42 0.20734714 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
43 0.15630399 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
44 0.20435938 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
45 0.17243579 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
46 0.19940512 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
201 0.23395776 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
202 0.26668772 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
203 0.20075050 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
204 0.20359058 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
209 0.14171092 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
210 0.10894524 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
211 0.10343336 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
212 0.12656061 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
213 0.16003948 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
214 0.16723238 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
217 0.17389017 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
218 0.17731455 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
219 0.11970041 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
220 0.12325040 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
221 0.09464757 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
222 0.17251257 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
225 0.16551289 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
229 0.16361168 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
230 0.08958169 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
235 0.16157814 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
237 0.24227673 -0.04293839 -0.05427982 0.4216415 0.7314692 0.410614 0.4107566 0.3959546 0.01925084
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months12 SpeciesPorites compressa:Months17
3 0.04580488 0.04514383 0.1557721
4 0.04580488 0.04514383 0.1557721
11 0.04580488 0.04514383 0.1557721
12 0.04580488 0.04514383 0.1557721
19 0.04580488 0.04514383 0.1557721
20 0.04580488 0.04514383 0.1557721
26 0.04580488 0.04514383 0.1557721
27 0.04580488 0.04514383 0.1557721
41 0.04580488 0.04514383 0.1557721
42 0.04580488 0.04514383 0.1557721
43 0.04580488 0.04514383 0.1557721
44 0.04580488 0.04514383 0.1557721
45 0.04580488 0.04514383 0.1557721
46 0.04580488 0.04514383 0.1557721
201 0.04580488 0.04514383 0.1557721
202 0.04580488 0.04514383 0.1557721
203 0.04580488 0.04514383 0.1557721
204 0.04580488 0.04514383 0.1557721
209 0.04580488 0.04514383 0.1557721
210 0.04580488 0.04514383 0.1557721
211 0.04580488 0.04514383 0.1557721
212 0.04580488 0.04514383 0.1557721
213 0.04580488 0.04514383 0.1557721
214 0.04580488 0.04514383 0.1557721
217 0.04580488 0.04514383 0.1557721
218 0.04580488 0.04514383 0.1557721
219 0.04580488 0.04514383 0.1557721
220 0.04580488 0.04514383 0.1557721
221 0.04580488 0.04514383 0.1557721
222 0.04580488 0.04514383 0.1557721
225 0.04580488 0.04514383 0.1557721
229 0.04580488 0.04514383 0.1557721
230 0.04580488 0.04514383 0.1557721
235 0.04580488 0.04514383 0.1557721
237 0.04580488 0.04514383 0.1557721
SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35
3 0.2083996 0.202875 0.3153576 0.06295488
4 0.2083996 0.202875 0.3153576 0.06295488
11 0.2083996 0.202875 0.3153576 0.06295488
12 0.2083996 0.202875 0.3153576 0.06295488
19 0.2083996 0.202875 0.3153576 0.06295488
20 0.2083996 0.202875 0.3153576 0.06295488
26 0.2083996 0.202875 0.3153576 0.06295488
27 0.2083996 0.202875 0.3153576 0.06295488
41 0.2083996 0.202875 0.3153576 0.06295488
42 0.2083996 0.202875 0.3153576 0.06295488
43 0.2083996 0.202875 0.3153576 0.06295488
44 0.2083996 0.202875 0.3153576 0.06295488
45 0.2083996 0.202875 0.3153576 0.06295488
46 0.2083996 0.202875 0.3153576 0.06295488
201 0.2083996 0.202875 0.3153576 0.06295488
202 0.2083996 0.202875 0.3153576 0.06295488
203 0.2083996 0.202875 0.3153576 0.06295488
204 0.2083996 0.202875 0.3153576 0.06295488
209 0.2083996 0.202875 0.3153576 0.06295488
210 0.2083996 0.202875 0.3153576 0.06295488
211 0.2083996 0.202875 0.3153576 0.06295488
212 0.2083996 0.202875 0.3153576 0.06295488
213 0.2083996 0.202875 0.3153576 0.06295488
214 0.2083996 0.202875 0.3153576 0.06295488
217 0.2083996 0.202875 0.3153576 0.06295488
218 0.2083996 0.202875 0.3153576 0.06295488
219 0.2083996 0.202875 0.3153576 0.06295488
220 0.2083996 0.202875 0.3153576 0.06295488
221 0.2083996 0.202875 0.3153576 0.06295488
222 0.2083996 0.202875 0.3153576 0.06295488
225 0.2083996 0.202875 0.3153576 0.06295488
229 0.2083996 0.202875 0.3153576 0.06295488
230 0.2083996 0.202875 0.3153576 0.06295488
235 0.2083996 0.202875 0.3153576 0.06295488
237 0.2083996 0.202875 0.3153576 0.06295488
BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20 BleachNon-bleach:Months24 BleachNon-bleach:Months29
3 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
4 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
11 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
12 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
19 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
20 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
26 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
27 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
41 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
42 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
43 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
44 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
45 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
46 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
201 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
202 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
203 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
204 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
209 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
210 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
211 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
212 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
213 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
214 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
217 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
218 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
219 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
220 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
221 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
222 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
225 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
229 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
230 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
235 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
237 0.04292905 0.3080971 -0.06603032 -0.04129801 0.1171523
BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 0.04694947 0.415676 -0.3398956
4 0.04694947 0.415676 -0.3398956
11 0.04694947 0.415676 -0.3398956
12 0.04694947 0.415676 -0.3398956
19 0.04694947 0.415676 -0.3398956
20 0.04694947 0.415676 -0.3398956
26 0.04694947 0.415676 -0.3398956
27 0.04694947 0.415676 -0.3398956
41 0.04694947 0.415676 -0.3398956
42 0.04694947 0.415676 -0.3398956
43 0.04694947 0.415676 -0.3398956
44 0.04694947 0.415676 -0.3398956
45 0.04694947 0.415676 -0.3398956
46 0.04694947 0.415676 -0.3398956
201 0.04694947 0.415676 -0.3398956
202 0.04694947 0.415676 -0.3398956
203 0.04694947 0.415676 -0.3398956
204 0.04694947 0.415676 -0.3398956
209 0.04694947 0.415676 -0.3398956
210 0.04694947 0.415676 -0.3398956
211 0.04694947 0.415676 -0.3398956
212 0.04694947 0.415676 -0.3398956
213 0.04694947 0.415676 -0.3398956
214 0.04694947 0.415676 -0.3398956
217 0.04694947 0.415676 -0.3398956
218 0.04694947 0.415676 -0.3398956
219 0.04694947 0.415676 -0.3398956
220 0.04694947 0.415676 -0.3398956
221 0.04694947 0.415676 -0.3398956
222 0.04694947 0.415676 -0.3398956
225 0.04694947 0.415676 -0.3398956
229 0.04694947 0.415676 -0.3398956
230 0.04694947 0.415676 -0.3398956
235 0.04694947 0.415676 -0.3398956
237 0.04694947 0.415676 -0.3398956
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 -0.06087927 0.2395837
4 -0.06087927 0.2395837
11 -0.06087927 0.2395837
12 -0.06087927 0.2395837
19 -0.06087927 0.2395837
20 -0.06087927 0.2395837
26 -0.06087927 0.2395837
27 -0.06087927 0.2395837
41 -0.06087927 0.2395837
42 -0.06087927 0.2395837
43 -0.06087927 0.2395837
44 -0.06087927 0.2395837
45 -0.06087927 0.2395837
46 -0.06087927 0.2395837
201 -0.06087927 0.2395837
202 -0.06087927 0.2395837
203 -0.06087927 0.2395837
204 -0.06087927 0.2395837
209 -0.06087927 0.2395837
210 -0.06087927 0.2395837
211 -0.06087927 0.2395837
212 -0.06087927 0.2395837
213 -0.06087927 0.2395837
214 -0.06087927 0.2395837
217 -0.06087927 0.2395837
218 -0.06087927 0.2395837
219 -0.06087927 0.2395837
220 -0.06087927 0.2395837
221 -0.06087927 0.2395837
222 -0.06087927 0.2395837
225 -0.06087927 0.2395837
229 -0.06087927 0.2395837
230 -0.06087927 0.2395837
235 -0.06087927 0.2395837
237 -0.06087927 0.2395837
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.3919705 -0.07755502
4 -0.3919705 -0.07755502
11 -0.3919705 -0.07755502
12 -0.3919705 -0.07755502
19 -0.3919705 -0.07755502
20 -0.3919705 -0.07755502
26 -0.3919705 -0.07755502
27 -0.3919705 -0.07755502
41 -0.3919705 -0.07755502
42 -0.3919705 -0.07755502
43 -0.3919705 -0.07755502
44 -0.3919705 -0.07755502
45 -0.3919705 -0.07755502
46 -0.3919705 -0.07755502
201 -0.3919705 -0.07755502
202 -0.3919705 -0.07755502
203 -0.3919705 -0.07755502
204 -0.3919705 -0.07755502
209 -0.3919705 -0.07755502
210 -0.3919705 -0.07755502
211 -0.3919705 -0.07755502
212 -0.3919705 -0.07755502
213 -0.3919705 -0.07755502
214 -0.3919705 -0.07755502
217 -0.3919705 -0.07755502
218 -0.3919705 -0.07755502
219 -0.3919705 -0.07755502
220 -0.3919705 -0.07755502
221 -0.3919705 -0.07755502
222 -0.3919705 -0.07755502
225 -0.3919705 -0.07755502
229 -0.3919705 -0.07755502
230 -0.3919705 -0.07755502
235 -0.3919705 -0.07755502
237 -0.3919705 -0.07755502
[ reached 'max' / getOption("max.print") -- omitted 7 rows ]###Figure
#ppo$Date<- as.Date(as.POSIXct(ppo$Date, origin="1970-01-01"))
ppofig<-ggplot(phys, aes(y=PPO, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
ppofig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
ppo_stress_fig<-ggplot(phys_stress, aes(y=PPO, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=PPO, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=PPO, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
geom_boxplot(alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
ppo_stress_fig
library(Rmisc)
ppo_sum<-summarySE(phys, measurevar='PPO', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedppo_sumppofig_3<-ggplot(ppo_sum, aes(y=PPO, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=ppo_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "ppo", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=PPO-se, ymax=PPO+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(0,1.25))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statppofig_3
##Pnet ###Normality
hist(phys$Pmax)
Pnet.lm<- lm(Pmax~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(Pnet.lm, ask=FALSE, which=1:6)
###Stats
Pnet.lme <- lme(Pmax~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(Pnet.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, Months12, Months17, Months20, SpeciesPorites compressa:Months10, SpeciesPorites compressa:Months12, SpeciesPorites compressa:Months17, SpeciesPorites compressa:Months20, BleachNon-bleach:Months10, BleachNon-bleach:Months12, BleachNon-bleach:Months17, BleachNon-bleach:Months20, SpeciesPorites compressa:BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months12, SpeciesPorites compressa:BleachNon-bleach:Months17, SpeciesPorites compressa:BleachNon-bleach:Months20Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Pmax
Chisq Df Pr(>Chisq)
(Intercept) 78.0618 1 < 2.2e-16 ***
Species 4.7354 1 0.029549 *
Bleach 0.9484 1 0.330127
Months 2.9853 3 0.393897
Species:Bleach 1.3964 1 0.237319
Species:Months 11.8151 3 0.008044 **
Bleach:Months 0.5269 3 0.912933
Species:Bleach:Months 5.9321 3 0.114962
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(Pnet.lme, list(pairwise ~ Months), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Months`
Months emmean SE df lower.CL upper.CL
0 2.71 0.118 44 2.48 2.95
24 2.68 0.130 44 2.42 2.95
29 2.89 0.130 44 2.62 3.15
35 2.71 0.118 44 2.48 2.95
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Months`
1 estimate SE df t.ratio p.value
Months0 - Months24 0.030025 0.159 82 0.188 0.9976
Months0 - Months29 -0.173940 0.159 82 -1.092 0.6957
Months0 - Months35 -0.000334 0.151 82 -0.002 1.0000
Months24 - Months29 -0.203965 0.165 82 -1.234 0.6070
Months24 - Months35 -0.030359 0.159 82 -0.191 0.9975
Months29 - Months35 0.173606 0.159 82 1.089 0.6970
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 4 estimates tukey3<- emmeans(Pnet.lme, list(pairwise ~Species:Months), adjust = "tukey", simple="Months")NOTE: Results may be misleading due to involvement in interactionstukey3 #no differences within Species and Bleach $`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 2.22 0.165 45 1.89 2.55
Porites compressa 0 3.21 0.169 44 2.87 3.55
Montipora capitata 24 1.81 0.173 45 1.46 2.16
Porites compressa 24 3.55 0.195 44 3.16 3.94
Montipora capitata 29 2.27 0.173 45 1.92 2.62
Porites compressa 29 3.50 0.195 44 3.11 3.89
Montipora capitata 35 2.11 0.165 45 1.77 2.44
Porites compressa 35 3.32 0.169 44 2.98 3.66
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Months0 - Months24 0.4039 0.214 82 1.885 0.2423
Months0 - Months29 -0.0563 0.214 82 -0.263 0.9936
Months0 - Months35 0.1108 0.210 82 0.529 0.9519
Months24 - Months29 -0.4602 0.219 82 -2.105 0.1600
Months24 - Months35 -0.2931 0.214 82 -1.368 0.5229
Months29 - Months35 0.1671 0.214 82 0.780 0.8632
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Months0 - Months24 -0.3439 0.236 82 -1.457 0.4679
Months0 - Months29 -0.2916 0.236 82 -1.236 0.6062
Months0 - Months35 -0.1115 0.218 82 -0.512 0.9561
Months24 - Months29 0.0523 0.248 82 0.211 0.9967
Months24 - Months35 0.2324 0.236 82 0.985 0.7585
Months29 - Months35 0.1801 0.236 82 0.763 0.8708
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 4 estimates summary(Pnet.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.3378076 0.6558163
Fixed effects: Pmax ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M24 SPc:M29 SPc:M3 BN-:M24 BN-:M29
SpeciesPorites compressa -0.710
BleachNon-bleach -0.707 0.502
Months24 -0.610 0.433 0.431
Months29 -0.610 0.433 0.431 0.479
Months35 -0.637 0.452 0.450 0.489 0.489
SpeciesPorites compressa:BleachNon-bleach 0.497 -0.696 -0.703 -0.303 -0.303 -0.316
SpeciesPorites compressa:Months24 0.412 -0.592 -0.291 -0.675 -0.323 -0.330 0.420
SpeciesPorites compressa:Months29 0.412 -0.592 -0.291 -0.323 -0.675 -0.330 0.420 0.458
SpeciesPorites compressa:Months35 0.448 -0.643 -0.317 -0.344 -0.344 -0.703 0.450 0.469 0.469
BleachNon-bleach:Months24 0.431 -0.306 -0.610 -0.707 -0.339 -0.346 0.429 0.477 0.229 0.243
BleachNon-bleach:Months29 0.431 -0.306 -0.610 -0.339 -0.707 -0.346 0.429 0.229 0.477 0.243 0.479
BleachNon-bleach:Months35 0.450 -0.320 -0.637 -0.346 -0.346 -0.707 0.448 0.233 0.233 0.497 0.489 0.489
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.287 0.418 0.406 0.471 0.226 0.230 -0.606 -0.705 -0.327 -0.327 -0.666 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.287 0.418 0.406 0.226 0.471 0.230 -0.606 -0.327 -0.705 -0.327 -0.319 -0.666
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.312 0.448 0.441 0.240 0.240 0.490 -0.646 -0.327 -0.327 -0.697 -0.339 -0.339
BN-:M3 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.326 0.473
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.693 0.470 0.470
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.36950502 -0.42003785 0.01543632 0.41858547 2.92307316
Number of Observations: 142
Number of Groups: 46 r.squaredGLMM(Pnet.lme) R2m R2c
[1,] 0.4768679 0.5865623####Coefficients
coef(Pnet.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months24 Months29 Months35 SpeciesPorites compressa:BleachNon-bleach
3 2.042975 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
4 2.165240 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
11 2.131658 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
12 1.971555 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
19 2.089157 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
20 2.090950 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
26 1.394689 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
27 2.109112 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
35 1.930132 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
36 2.149096 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
41 1.990711 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
42 1.818439 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
43 2.068922 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
44 1.795500 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
45 1.818021 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
46 1.970410 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
201 1.961452 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
202 2.231923 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
203 2.068824 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
204 2.067341 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
209 1.917495 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
210 2.025408 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
211 2.004383 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
212 1.982239 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
213 2.112488 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
214 2.063509 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
217 2.104896 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
218 2.013197 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
219 2.007239 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
220 1.945496 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
221 2.186770 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
222 2.070479 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
225 2.133621 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
226 1.961916 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
229 2.565654 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
230 2.183383 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
235 2.527450 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
236 2.174823 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
237 1.869670 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
238 2.370242 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
239 1.679782 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
240 2.530165 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
243 2.029432 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
244 2.315568 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
247 1.765987 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
248 2.216011 0.7136888 0.3206509 -0.376059 0.1138286 -0.1994816 0.553421
SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35 BleachNon-bleach:Months24
3 1.497114 0.4471068 0.3816755 -0.05574266
4 1.497114 0.4471068 0.3816755 -0.05574266
11 1.497114 0.4471068 0.3816755 -0.05574266
12 1.497114 0.4471068 0.3816755 -0.05574266
19 1.497114 0.4471068 0.3816755 -0.05574266
20 1.497114 0.4471068 0.3816755 -0.05574266
26 1.497114 0.4471068 0.3816755 -0.05574266
27 1.497114 0.4471068 0.3816755 -0.05574266
35 1.497114 0.4471068 0.3816755 -0.05574266
36 1.497114 0.4471068 0.3816755 -0.05574266
41 1.497114 0.4471068 0.3816755 -0.05574266
42 1.497114 0.4471068 0.3816755 -0.05574266
43 1.497114 0.4471068 0.3816755 -0.05574266
44 1.497114 0.4471068 0.3816755 -0.05574266
45 1.497114 0.4471068 0.3816755 -0.05574266
46 1.497114 0.4471068 0.3816755 -0.05574266
201 1.497114 0.4471068 0.3816755 -0.05574266
202 1.497114 0.4471068 0.3816755 -0.05574266
203 1.497114 0.4471068 0.3816755 -0.05574266
204 1.497114 0.4471068 0.3816755 -0.05574266
209 1.497114 0.4471068 0.3816755 -0.05574266
210 1.497114 0.4471068 0.3816755 -0.05574266
211 1.497114 0.4471068 0.3816755 -0.05574266
212 1.497114 0.4471068 0.3816755 -0.05574266
213 1.497114 0.4471068 0.3816755 -0.05574266
214 1.497114 0.4471068 0.3816755 -0.05574266
217 1.497114 0.4471068 0.3816755 -0.05574266
218 1.497114 0.4471068 0.3816755 -0.05574266
219 1.497114 0.4471068 0.3816755 -0.05574266
220 1.497114 0.4471068 0.3816755 -0.05574266
221 1.497114 0.4471068 0.3816755 -0.05574266
222 1.497114 0.4471068 0.3816755 -0.05574266
225 1.497114 0.4471068 0.3816755 -0.05574266
226 1.497114 0.4471068 0.3816755 -0.05574266
229 1.497114 0.4471068 0.3816755 -0.05574266
230 1.497114 0.4471068 0.3816755 -0.05574266
235 1.497114 0.4471068 0.3816755 -0.05574266
236 1.497114 0.4471068 0.3816755 -0.05574266
237 1.497114 0.4471068 0.3816755 -0.05574266
238 1.497114 0.4471068 0.3816755 -0.05574266
239 1.497114 0.4471068 0.3816755 -0.05574266
240 1.497114 0.4471068 0.3816755 -0.05574266
243 1.497114 0.4471068 0.3816755 -0.05574266
244 1.497114 0.4471068 0.3816755 -0.05574266
247 1.497114 0.4471068 0.3816755 -0.05574266
248 1.497114 0.4471068 0.3816755 -0.05574266
BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months24
3 -0.1150532 0.1772857 -1.498607
4 -0.1150532 0.1772857 -1.498607
11 -0.1150532 0.1772857 -1.498607
12 -0.1150532 0.1772857 -1.498607
19 -0.1150532 0.1772857 -1.498607
20 -0.1150532 0.1772857 -1.498607
26 -0.1150532 0.1772857 -1.498607
27 -0.1150532 0.1772857 -1.498607
35 -0.1150532 0.1772857 -1.498607
36 -0.1150532 0.1772857 -1.498607
41 -0.1150532 0.1772857 -1.498607
42 -0.1150532 0.1772857 -1.498607
43 -0.1150532 0.1772857 -1.498607
44 -0.1150532 0.1772857 -1.498607
45 -0.1150532 0.1772857 -1.498607
46 -0.1150532 0.1772857 -1.498607
201 -0.1150532 0.1772857 -1.498607
202 -0.1150532 0.1772857 -1.498607
203 -0.1150532 0.1772857 -1.498607
204 -0.1150532 0.1772857 -1.498607
209 -0.1150532 0.1772857 -1.498607
210 -0.1150532 0.1772857 -1.498607
211 -0.1150532 0.1772857 -1.498607
212 -0.1150532 0.1772857 -1.498607
213 -0.1150532 0.1772857 -1.498607
214 -0.1150532 0.1772857 -1.498607
217 -0.1150532 0.1772857 -1.498607
218 -0.1150532 0.1772857 -1.498607
219 -0.1150532 0.1772857 -1.498607
220 -0.1150532 0.1772857 -1.498607
221 -0.1150532 0.1772857 -1.498607
222 -0.1150532 0.1772857 -1.498607
225 -0.1150532 0.1772857 -1.498607
226 -0.1150532 0.1772857 -1.498607
229 -0.1150532 0.1772857 -1.498607
230 -0.1150532 0.1772857 -1.498607
235 -0.1150532 0.1772857 -1.498607
236 -0.1150532 0.1772857 -1.498607
237 -0.1150532 0.1772857 -1.498607
238 -0.1150532 0.1772857 -1.498607
239 -0.1150532 0.1772857 -1.498607
240 -0.1150532 0.1772857 -1.498607
243 -0.1150532 0.1772857 -1.498607
244 -0.1150532 0.1772857 -1.498607
247 -0.1150532 0.1772857 -1.498607
248 -0.1150532 0.1772857 -1.498607
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.4236605 -0.3186589
4 -0.4236605 -0.3186589
11 -0.4236605 -0.3186589
12 -0.4236605 -0.3186589
19 -0.4236605 -0.3186589
20 -0.4236605 -0.3186589
26 -0.4236605 -0.3186589
27 -0.4236605 -0.3186589
35 -0.4236605 -0.3186589
36 -0.4236605 -0.3186589
41 -0.4236605 -0.3186589
42 -0.4236605 -0.3186589
43 -0.4236605 -0.3186589
44 -0.4236605 -0.3186589
45 -0.4236605 -0.3186589
46 -0.4236605 -0.3186589
201 -0.4236605 -0.3186589
202 -0.4236605 -0.3186589
203 -0.4236605 -0.3186589
204 -0.4236605 -0.3186589
209 -0.4236605 -0.3186589
210 -0.4236605 -0.3186589
211 -0.4236605 -0.3186589
212 -0.4236605 -0.3186589
213 -0.4236605 -0.3186589
214 -0.4236605 -0.3186589
217 -0.4236605 -0.3186589
218 -0.4236605 -0.3186589
219 -0.4236605 -0.3186589
220 -0.4236605 -0.3186589
221 -0.4236605 -0.3186589
222 -0.4236605 -0.3186589
225 -0.4236605 -0.3186589
226 -0.4236605 -0.3186589
229 -0.4236605 -0.3186589
230 -0.4236605 -0.3186589
235 -0.4236605 -0.3186589
236 -0.4236605 -0.3186589
237 -0.4236605 -0.3186589
238 -0.4236605 -0.3186589
239 -0.4236605 -0.3186589
240 -0.4236605 -0.3186589
243 -0.4236605 -0.3186589
244 -0.4236605 -0.3186589
247 -0.4236605 -0.3186589
248 -0.4236605 -0.3186589###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
Pnetfig<-ggplot(phys, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
Pnetfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
Pnetfig2<-ggplot(phys, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
Pnetfig2
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
pnet_stress_fig<-ggplot(phys_stress, aes(y=Pmax, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=Pmax, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=Pmax, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
pnet_stress_fig
library(Rmisc)
Pnet_sum<-summarySE(phys, measurevar='Pmax', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedPnet_sumPnetfig_3<-ggplot(Pnet_sum, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=Pnet_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "Pnet", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=Pmax-se, ymax=Pmax+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Gross~photosynthesis~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(0,4))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statPnetfig_3
##LEDR ###Normality
hist(phys$R)
LEDR.lm<- lm(R~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(LEDR.lm, ask=FALSE, which=1:6)
###Stats
LEDR.lme <- lme(R~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(LEDR.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, Months12, Months17, Months20, SpeciesPorites compressa:Months10, SpeciesPorites compressa:Months12, SpeciesPorites compressa:Months17, SpeciesPorites compressa:Months20, BleachNon-bleach:Months10, BleachNon-bleach:Months12, BleachNon-bleach:Months17, BleachNon-bleach:Months20, SpeciesPorites compressa:BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months12, SpeciesPorites compressa:BleachNon-bleach:Months17, SpeciesPorites compressa:BleachNon-bleach:Months20Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: R
Chisq Df Pr(>Chisq)
(Intercept) 30.5103 1 3.321e-08 ***
Species 3.3466 1 0.06734 .
Bleach 2.4318 1 0.11890
Months 1.3807 3 0.71007
Species:Bleach 0.6855 1 0.40770
Species:Months 8.0380 3 0.04523 *
Bleach:Months 2.8014 3 0.42326
Species:Bleach:Months 5.4296 3 0.14291
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(LEDR.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Species")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Months`
Species Months emmean SE df lower.CL upper.CL
Montipora capitata 0 -0.550 0.0587 45 -0.668 -0.431
Porites compressa 0 -0.831 0.0585 44 -0.949 -0.713
Montipora capitata 24 -0.399 0.0616 45 -0.523 -0.275
Porites compressa 24 -0.851 0.0692 44 -0.990 -0.711
Montipora capitata 29 -0.420 0.0616 45 -0.544 -0.296
Porites compressa 29 -0.893 0.0692 44 -1.033 -0.754
Montipora capitata 35 -0.543 0.0587 45 -0.661 -0.425
Porites compressa 35 -0.831 0.0585 44 -0.949 -0.713
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Months | Months`
Months = 0:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.282 0.0829 44 3.399 0.0014
Months = 24:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.452 0.0927 44 4.871 <.0001
Months = 29:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.473 0.0927 44 5.102 <.0001
Months = 35:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.288 0.0829 44 3.475 0.0012
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment summary(LEDR.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.1271718 0.2301499
Fixed effects: R ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M24 SPc:M29 SPc:M3 BN-:M24 BN-:M29
SpeciesPorites compressa -0.711
BleachNon-bleach -0.707 0.502
Months24 -0.601 0.427 0.425
Months29 -0.601 0.427 0.425 0.480
Months35 -0.628 0.446 0.444 0.489 0.489
SpeciesPorites compressa:BleachNon-bleach 0.504 -0.704 -0.713 -0.303 -0.303 -0.317
SpeciesPorites compressa:Months24 0.405 -0.584 -0.286 -0.674 -0.324 -0.330 0.420
SpeciesPorites compressa:Months29 0.405 -0.584 -0.286 -0.324 -0.674 -0.330 0.420 0.460
SpeciesPorites compressa:Months35 0.441 -0.635 -0.312 -0.344 -0.344 -0.703 0.451 0.469 0.469
BleachNon-bleach:Months24 0.425 -0.302 -0.601 -0.707 -0.339 -0.346 0.428 0.477 0.229 0.243
BleachNon-bleach:Months29 0.425 -0.302 -0.601 -0.339 -0.707 -0.346 0.428 0.229 0.477 0.243 0.480
BleachNon-bleach:Months35 0.444 -0.315 -0.628 -0.346 -0.346 -0.707 0.448 0.233 0.233 0.497 0.489 0.489
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.285 0.416 0.403 0.474 0.228 0.232 -0.591 -0.711 -0.331 -0.330 -0.671 -0.322
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.285 0.416 0.403 0.228 0.474 0.232 -0.591 -0.331 -0.711 -0.330 -0.322 -0.671
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.312 0.449 0.441 0.243 0.243 0.497 -0.637 -0.332 -0.332 -0.707 -0.344 -0.344
BN-:M3 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.328
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.328 0.465
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.703 0.467 0.467
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.583751417 -0.370110920 -0.003151921 0.520709248 2.451005709
Number of Observations: 144
Number of Groups: 46 r.squaredGLMM(LEDR.lme) R2m R2c
[1,] 0.4073081 0.5459426####Coefficients
coef(LEDR.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months24 Months29 Months35 SpeciesPorites compressa:BleachNon-bleach
3 -0.4664579 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
4 -0.5075512 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
11 -0.5154915 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
12 -0.4352650 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
19 -0.4912221 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
20 -0.4386677 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
26 -0.2810275 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
27 -0.5503831 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
35 -0.4059624 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
36 -0.3666854 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
41 -0.4021131 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
42 -0.2687893 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
43 -0.4771389 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
44 -0.4143611 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
45 -0.4286228 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
46 -0.5101641 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
201 -0.4272415 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
202 -0.5505554 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
203 -0.4428208 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
204 -0.4656099 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
209 -0.3767881 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
210 -0.4338141 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
211 -0.4258001 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
212 -0.4596166 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
213 -0.4945142 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
214 -0.4753819 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
217 -0.4891664 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
218 -0.4435274 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
219 -0.4488075 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
220 -0.4111539 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
221 -0.4614930 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
222 -0.4186600 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
225 -0.4536918 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
226 -0.4136937 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
229 -0.5580496 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
230 -0.4730123 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
235 -0.5477629 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
236 -0.4833550 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
237 -0.5049127 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
238 -0.5776921 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
239 -0.3525914 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
240 -0.7342246 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
243 -0.4167589 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
244 -0.6447028 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
247 -0.3445995 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
248 -0.3856392 -0.2135541 -0.1829263 0.1239964 0.04817312 0.0482568 -0.1361523
SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29 SpeciesPorites compressa:Months35 BleachNon-bleach:Months24
3 -0.4213275 -0.2455119 -0.09223455 0.0526974
4 -0.4213275 -0.2455119 -0.09223455 0.0526974
11 -0.4213275 -0.2455119 -0.09223455 0.0526974
12 -0.4213275 -0.2455119 -0.09223455 0.0526974
19 -0.4213275 -0.2455119 -0.09223455 0.0526974
20 -0.4213275 -0.2455119 -0.09223455 0.0526974
26 -0.4213275 -0.2455119 -0.09223455 0.0526974
27 -0.4213275 -0.2455119 -0.09223455 0.0526974
35 -0.4213275 -0.2455119 -0.09223455 0.0526974
36 -0.4213275 -0.2455119 -0.09223455 0.0526974
41 -0.4213275 -0.2455119 -0.09223455 0.0526974
42 -0.4213275 -0.2455119 -0.09223455 0.0526974
43 -0.4213275 -0.2455119 -0.09223455 0.0526974
44 -0.4213275 -0.2455119 -0.09223455 0.0526974
45 -0.4213275 -0.2455119 -0.09223455 0.0526974
46 -0.4213275 -0.2455119 -0.09223455 0.0526974
201 -0.4213275 -0.2455119 -0.09223455 0.0526974
202 -0.4213275 -0.2455119 -0.09223455 0.0526974
203 -0.4213275 -0.2455119 -0.09223455 0.0526974
204 -0.4213275 -0.2455119 -0.09223455 0.0526974
209 -0.4213275 -0.2455119 -0.09223455 0.0526974
210 -0.4213275 -0.2455119 -0.09223455 0.0526974
211 -0.4213275 -0.2455119 -0.09223455 0.0526974
212 -0.4213275 -0.2455119 -0.09223455 0.0526974
213 -0.4213275 -0.2455119 -0.09223455 0.0526974
214 -0.4213275 -0.2455119 -0.09223455 0.0526974
217 -0.4213275 -0.2455119 -0.09223455 0.0526974
218 -0.4213275 -0.2455119 -0.09223455 0.0526974
219 -0.4213275 -0.2455119 -0.09223455 0.0526974
220 -0.4213275 -0.2455119 -0.09223455 0.0526974
221 -0.4213275 -0.2455119 -0.09223455 0.0526974
222 -0.4213275 -0.2455119 -0.09223455 0.0526974
225 -0.4213275 -0.2455119 -0.09223455 0.0526974
226 -0.4213275 -0.2455119 -0.09223455 0.0526974
229 -0.4213275 -0.2455119 -0.09223455 0.0526974
230 -0.4213275 -0.2455119 -0.09223455 0.0526974
235 -0.4213275 -0.2455119 -0.09223455 0.0526974
236 -0.4213275 -0.2455119 -0.09223455 0.0526974
237 -0.4213275 -0.2455119 -0.09223455 0.0526974
238 -0.4213275 -0.2455119 -0.09223455 0.0526974
239 -0.4213275 -0.2455119 -0.09223455 0.0526974
240 -0.4213275 -0.2455119 -0.09223455 0.0526974
243 -0.4213275 -0.2455119 -0.09223455 0.0526974
244 -0.4213275 -0.2455119 -0.09223455 0.0526974
247 -0.4213275 -0.2455119 -0.09223455 0.0526974
248 -0.4213275 -0.2455119 -0.09223455 0.0526974
BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months24
3 0.1624192 -0.08355351 0.5028243
4 0.1624192 -0.08355351 0.5028243
11 0.1624192 -0.08355351 0.5028243
12 0.1624192 -0.08355351 0.5028243
19 0.1624192 -0.08355351 0.5028243
20 0.1624192 -0.08355351 0.5028243
26 0.1624192 -0.08355351 0.5028243
27 0.1624192 -0.08355351 0.5028243
35 0.1624192 -0.08355351 0.5028243
36 0.1624192 -0.08355351 0.5028243
41 0.1624192 -0.08355351 0.5028243
42 0.1624192 -0.08355351 0.5028243
43 0.1624192 -0.08355351 0.5028243
44 0.1624192 -0.08355351 0.5028243
45 0.1624192 -0.08355351 0.5028243
46 0.1624192 -0.08355351 0.5028243
201 0.1624192 -0.08355351 0.5028243
202 0.1624192 -0.08355351 0.5028243
203 0.1624192 -0.08355351 0.5028243
204 0.1624192 -0.08355351 0.5028243
209 0.1624192 -0.08355351 0.5028243
210 0.1624192 -0.08355351 0.5028243
211 0.1624192 -0.08355351 0.5028243
212 0.1624192 -0.08355351 0.5028243
213 0.1624192 -0.08355351 0.5028243
214 0.1624192 -0.08355351 0.5028243
217 0.1624192 -0.08355351 0.5028243
218 0.1624192 -0.08355351 0.5028243
219 0.1624192 -0.08355351 0.5028243
220 0.1624192 -0.08355351 0.5028243
221 0.1624192 -0.08355351 0.5028243
222 0.1624192 -0.08355351 0.5028243
225 0.1624192 -0.08355351 0.5028243
226 0.1624192 -0.08355351 0.5028243
229 0.1624192 -0.08355351 0.5028243
230 0.1624192 -0.08355351 0.5028243
235 0.1624192 -0.08355351 0.5028243
236 0.1624192 -0.08355351 0.5028243
237 0.1624192 -0.08355351 0.5028243
238 0.1624192 -0.08355351 0.5028243
239 0.1624192 -0.08355351 0.5028243
240 0.1624192 -0.08355351 0.5028243
243 0.1624192 -0.08355351 0.5028243
244 0.1624192 -0.08355351 0.5028243
247 0.1624192 -0.08355351 0.5028243
248 0.1624192 -0.08355351 0.5028243
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 0.1082819 0.1717485
4 0.1082819 0.1717485
11 0.1082819 0.1717485
12 0.1082819 0.1717485
19 0.1082819 0.1717485
20 0.1082819 0.1717485
26 0.1082819 0.1717485
27 0.1082819 0.1717485
35 0.1082819 0.1717485
36 0.1082819 0.1717485
41 0.1082819 0.1717485
42 0.1082819 0.1717485
43 0.1082819 0.1717485
44 0.1082819 0.1717485
45 0.1082819 0.1717485
46 0.1082819 0.1717485
201 0.1082819 0.1717485
202 0.1082819 0.1717485
203 0.1082819 0.1717485
204 0.1082819 0.1717485
209 0.1082819 0.1717485
210 0.1082819 0.1717485
211 0.1082819 0.1717485
212 0.1082819 0.1717485
213 0.1082819 0.1717485
214 0.1082819 0.1717485
217 0.1082819 0.1717485
218 0.1082819 0.1717485
219 0.1082819 0.1717485
220 0.1082819 0.1717485
221 0.1082819 0.1717485
222 0.1082819 0.1717485
225 0.1082819 0.1717485
226 0.1082819 0.1717485
229 0.1082819 0.1717485
230 0.1082819 0.1717485
235 0.1082819 0.1717485
236 0.1082819 0.1717485
237 0.1082819 0.1717485
238 0.1082819 0.1717485
239 0.1082819 0.1717485
240 0.1082819 0.1717485
243 0.1082819 0.1717485
244 0.1082819 0.1717485
247 0.1082819 0.1717485
248 0.1082819 0.1717485###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDRfig<-ggplot(phys, aes(y=R, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
LEDRfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDRfig2<-ggplot(phys, aes(y=R, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
LEDRfig2
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDR_stress_fig<-ggplot(phys_stress, aes(y=R, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=R, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=R, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
LEDR_stress_fig
library(Rmisc)
LEDR_sum<-summarySE(phys, measurevar='R', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedLEDR_sumLEDRfig_3<-ggplot(LEDR_sum, aes(y=abs(R), x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=LEDR_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "LEDR", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=abs(R)-se, ymax=abs(R)+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
#geom_hline(yintercept = 0, size=0.75, color = "black") +
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statLEDRfig_3
##alpha ###Normality
hist(phys$alpha)
alpha.lm<- lm(alpha~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(alpha.lm, ask=FALSE, which=1:6)
###Stats
alpha.lme <- lme(alpha~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(alpha.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, Months12, Months17, Months20, SpeciesPorites compressa:Months10, SpeciesPorites compressa:Months12, SpeciesPorites compressa:Months17, SpeciesPorites compressa:Months20, BleachNon-bleach:Months10, BleachNon-bleach:Months12, BleachNon-bleach:Months17, BleachNon-bleach:Months20, SpeciesPorites compressa:BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months12, SpeciesPorites compressa:BleachNon-bleach:Months17, SpeciesPorites compressa:BleachNon-bleach:Months20Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: alpha
Chisq Df Pr(>Chisq)
(Intercept) 25.0011 1 5.73e-07 ***
Species 0.6978 1 0.4035
Bleach 0.6243 1 0.4294
Months 4.2753 3 0.2332
Species:Bleach 1.7942 1 0.1804
Species:Months 4.3744 3 0.2238
Bleach:Months 0.8392 3 0.8401
Species:Bleach:Months 6.1724 3 0.1035
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(alpha.lme, list(pairwise ~ Months), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Months`
Months emmean SE df lower.CL upper.CL
0 0.00566 0.000415 44 0.00482 0.00650
24 0.00331 0.000462 44 0.00238 0.00424
29 0.00649 0.000462 44 0.00556 0.00742
35 0.00561 0.000415 44 0.00477 0.00644
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Months`
1 estimate SE df t.ratio p.value
Months0 - Months24 2.35e-03 0.000527 84 4.453 0.0002
Months0 - Months29 -8.28e-04 0.000527 84 -1.572 0.3999
Months0 - Months35 5.24e-05 0.000498 84 0.105 0.9996
Months24 - Months29 -3.17e-03 0.000548 84 -5.795 <.0001
Months24 - Months35 -2.29e-03 0.000527 84 -4.353 0.0002
Months29 - Months35 8.81e-04 0.000527 84 1.672 0.3449
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 4 estimates ###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alphafig<-ggplot(phys, aes(y=alpha, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
alphafig
###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alphafig2<-ggplot(phys, aes(y=alpha, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
alphafig2
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alpha_stress_fig<-ggplot(phys_stress, aes(y=alpha, x=Months, color=Bleach, fill=Bleach))+
#geom_point(alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
geom_boxplot(alpha=0.6, outlier.shape = NA)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
alpha_stress_fig
##P:R ###Normality
hist(phys$PR)
PR.lm<- lm(PR~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(PR.lm, ask=FALSE, which=1:6)
###Stats
PR.lme <- lme(PR~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(PR.lme, type=3)Warning: The following coefficients are not in the model due to missing levels:
Months10, Months12, Months17, Months20, SpeciesPorites compressa:Months10, SpeciesPorites compressa:Months12, SpeciesPorites compressa:Months17, SpeciesPorites compressa:Months20, BleachNon-bleach:Months10, BleachNon-bleach:Months12, BleachNon-bleach:Months17, BleachNon-bleach:Months20, SpeciesPorites compressa:BleachNon-bleach:Months10, SpeciesPorites compressa:BleachNon-bleach:Months12, SpeciesPorites compressa:BleachNon-bleach:Months17, SpeciesPorites compressa:BleachNon-bleach:Months20Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: PR
Chisq Df Pr(>Chisq)
(Intercept) 143.5030 1 < 2e-16 ***
Species 0.4413 1 0.50651
Bleach 4.1415 1 0.04184 *
Months 1.0204 3 0.79632
Species:Bleach 0.5789 1 0.44675
Species:Months 2.5281 3 0.47024
Bleach:Months 5.6824 3 0.12812
Species:Bleach:Months 1.2713 3 0.73596
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(PR.lme, list(pairwise ~ Bleach ), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Bleach`
Bleach emmean SE df lower.CL upper.CL
Bleach 4.68 0.178 44 4.32 5.04
Non-bleach 4.29 0.179 44 3.93 4.65
Results are averaged over the levels of: Species, Months
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Bleach`
1 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 0.384 0.25 81 1.535 0.1287
Results are averaged over the levels of: Species, Months
Degrees-of-freedom method: containment summary(PR.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.4681967 1.210518
Fixed effects: PR ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M24 SPc:M29 SPc:M3 BN-:M24 BN-:M29
SpeciesPorites compressa -0.708
BleachNon-bleach -0.707 0.501
Months24 -0.618 0.438 0.437
Months29 -0.640 0.453 0.453 0.461
Months35 -0.664 0.470 0.470 0.471 0.488
SpeciesPorites compressa:BleachNon-bleach 0.495 -0.697 -0.700 -0.306 -0.317 -0.329
SpeciesPorites compressa:Months24 0.427 -0.609 -0.302 -0.690 -0.318 -0.325 0.429
SpeciesPorites compressa:Months29 0.434 -0.619 -0.307 -0.312 -0.677 -0.331 0.436 0.445
SpeciesPorites compressa:Months35 0.468 -0.668 -0.331 -0.332 -0.344 -0.705 0.466 0.461 0.469
BleachNon-bleach:Months24 0.445 -0.315 -0.629 -0.719 -0.332 -0.339 0.440 0.496 0.224 0.239
BleachNon-bleach:Months29 0.453 -0.321 -0.640 -0.326 -0.707 -0.345 0.448 0.225 0.479 0.243 0.469
BleachNon-bleach:Months35 0.470 -0.333 -0.664 -0.333 -0.345 -0.707 0.465 0.230 0.234 0.498 0.480 0.488
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.301 0.433 0.425 0.486 0.224 0.229 -0.625 -0.710 -0.319 -0.325 -0.676 -0.317
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.303 0.436 0.429 0.218 0.474 0.231 -0.630 -0.316 -0.704 -0.328 -0.314 -0.670
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.326 0.465 0.462 0.232 0.240 0.491 -0.669 -0.322 -0.327 -0.697 -0.333 -0.339
BN-:M3 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.324
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.327 0.460
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.695 0.467 0.471
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-1.47685905 -0.57725141 -0.04417195 0.29168988 4.75280716
Number of Observations: 141
Number of Groups: 46 r.squaredGLMM(PR.lme) R2m R2c
[1,] 0.1881412 0.2937866####Coefficients
coef(protein.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 0.1759040 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
4 0.2218443 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
11 0.1824086 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
12 0.1432800 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
19 0.1650566 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
20 0.1370136 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
26 0.1585332 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
27 0.1552725 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
35 0.1759826 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
36 0.1632939 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
41 0.2291232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
42 0.1574232 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
43 0.1611075 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
44 0.1136417 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
45 0.2021523 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
46 0.1381121 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
201 0.1377209 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
202 0.1370790 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
203 0.1878345 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
204 0.1747205 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
209 0.1539102 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
210 0.1453911 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
211 0.1763872 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
212 0.2245608 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
213 0.1717698 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
214 0.1646707 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
217 0.1835225 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
218 0.1927358 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
219 0.1975645 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
220 0.1905783 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
221 0.1721688 0.1232805 -0.01530227 0.1444644 0.07799421 0.03415552 0.1129223 0.1332215 0.218622 0.2860489
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 -0.02228106 -0.03772763 -0.02605817
4 -0.02228106 -0.03772763 -0.02605817
11 -0.02228106 -0.03772763 -0.02605817
12 -0.02228106 -0.03772763 -0.02605817
19 -0.02228106 -0.03772763 -0.02605817
20 -0.02228106 -0.03772763 -0.02605817
26 -0.02228106 -0.03772763 -0.02605817
27 -0.02228106 -0.03772763 -0.02605817
35 -0.02228106 -0.03772763 -0.02605817
36 -0.02228106 -0.03772763 -0.02605817
41 -0.02228106 -0.03772763 -0.02605817
42 -0.02228106 -0.03772763 -0.02605817
43 -0.02228106 -0.03772763 -0.02605817
44 -0.02228106 -0.03772763 -0.02605817
45 -0.02228106 -0.03772763 -0.02605817
46 -0.02228106 -0.03772763 -0.02605817
201 -0.02228106 -0.03772763 -0.02605817
202 -0.02228106 -0.03772763 -0.02605817
203 -0.02228106 -0.03772763 -0.02605817
204 -0.02228106 -0.03772763 -0.02605817
209 -0.02228106 -0.03772763 -0.02605817
210 -0.02228106 -0.03772763 -0.02605817
211 -0.02228106 -0.03772763 -0.02605817
212 -0.02228106 -0.03772763 -0.02605817
213 -0.02228106 -0.03772763 -0.02605817
214 -0.02228106 -0.03772763 -0.02605817
217 -0.02228106 -0.03772763 -0.02605817
218 -0.02228106 -0.03772763 -0.02605817
219 -0.02228106 -0.03772763 -0.02605817
220 -0.02228106 -0.03772763 -0.02605817
221 -0.02228106 -0.03772763 -0.02605817
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 0.1174555 0.0586134 0.0903154 0.04990827
4 0.1174555 0.0586134 0.0903154 0.04990827
11 0.1174555 0.0586134 0.0903154 0.04990827
12 0.1174555 0.0586134 0.0903154 0.04990827
19 0.1174555 0.0586134 0.0903154 0.04990827
20 0.1174555 0.0586134 0.0903154 0.04990827
26 0.1174555 0.0586134 0.0903154 0.04990827
27 0.1174555 0.0586134 0.0903154 0.04990827
35 0.1174555 0.0586134 0.0903154 0.04990827
36 0.1174555 0.0586134 0.0903154 0.04990827
41 0.1174555 0.0586134 0.0903154 0.04990827
42 0.1174555 0.0586134 0.0903154 0.04990827
43 0.1174555 0.0586134 0.0903154 0.04990827
44 0.1174555 0.0586134 0.0903154 0.04990827
45 0.1174555 0.0586134 0.0903154 0.04990827
46 0.1174555 0.0586134 0.0903154 0.04990827
201 0.1174555 0.0586134 0.0903154 0.04990827
202 0.1174555 0.0586134 0.0903154 0.04990827
203 0.1174555 0.0586134 0.0903154 0.04990827
204 0.1174555 0.0586134 0.0903154 0.04990827
209 0.1174555 0.0586134 0.0903154 0.04990827
210 0.1174555 0.0586134 0.0903154 0.04990827
211 0.1174555 0.0586134 0.0903154 0.04990827
212 0.1174555 0.0586134 0.0903154 0.04990827
213 0.1174555 0.0586134 0.0903154 0.04990827
214 0.1174555 0.0586134 0.0903154 0.04990827
217 0.1174555 0.0586134 0.0903154 0.04990827
218 0.1174555 0.0586134 0.0903154 0.04990827
219 0.1174555 0.0586134 0.0903154 0.04990827
220 0.1174555 0.0586134 0.0903154 0.04990827
221 0.1174555 0.0586134 0.0903154 0.04990827
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
4 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
11 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
12 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
19 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
20 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
26 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
27 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
35 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
36 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
41 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
42 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
43 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
44 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
45 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
46 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
201 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
202 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
203 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
204 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
209 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
210 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
211 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
212 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
213 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
214 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
217 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
218 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
219 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
220 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
221 -0.1745044 -0.02197116 0.04277125 0.1121015 0.05080975
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 0.08454026 0.05176502 0.03536143 -0.02947219
4 0.08454026 0.05176502 0.03536143 -0.02947219
11 0.08454026 0.05176502 0.03536143 -0.02947219
12 0.08454026 0.05176502 0.03536143 -0.02947219
19 0.08454026 0.05176502 0.03536143 -0.02947219
20 0.08454026 0.05176502 0.03536143 -0.02947219
26 0.08454026 0.05176502 0.03536143 -0.02947219
27 0.08454026 0.05176502 0.03536143 -0.02947219
35 0.08454026 0.05176502 0.03536143 -0.02947219
36 0.08454026 0.05176502 0.03536143 -0.02947219
41 0.08454026 0.05176502 0.03536143 -0.02947219
42 0.08454026 0.05176502 0.03536143 -0.02947219
43 0.08454026 0.05176502 0.03536143 -0.02947219
44 0.08454026 0.05176502 0.03536143 -0.02947219
45 0.08454026 0.05176502 0.03536143 -0.02947219
46 0.08454026 0.05176502 0.03536143 -0.02947219
201 0.08454026 0.05176502 0.03536143 -0.02947219
202 0.08454026 0.05176502 0.03536143 -0.02947219
203 0.08454026 0.05176502 0.03536143 -0.02947219
204 0.08454026 0.05176502 0.03536143 -0.02947219
209 0.08454026 0.05176502 0.03536143 -0.02947219
210 0.08454026 0.05176502 0.03536143 -0.02947219
211 0.08454026 0.05176502 0.03536143 -0.02947219
212 0.08454026 0.05176502 0.03536143 -0.02947219
213 0.08454026 0.05176502 0.03536143 -0.02947219
214 0.08454026 0.05176502 0.03536143 -0.02947219
217 0.08454026 0.05176502 0.03536143 -0.02947219
218 0.08454026 0.05176502 0.03536143 -0.02947219
219 0.08454026 0.05176502 0.03536143 -0.02947219
220 0.08454026 0.05176502 0.03536143 -0.02947219
221 0.08454026 0.05176502 0.03536143 -0.02947219
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 0.07407306 0.07902784
4 0.07407306 0.07902784
11 0.07407306 0.07902784
12 0.07407306 0.07902784
19 0.07407306 0.07902784
20 0.07407306 0.07902784
26 0.07407306 0.07902784
27 0.07407306 0.07902784
35 0.07407306 0.07902784
36 0.07407306 0.07902784
41 0.07407306 0.07902784
42 0.07407306 0.07902784
43 0.07407306 0.07902784
44 0.07407306 0.07902784
45 0.07407306 0.07902784
46 0.07407306 0.07902784
201 0.07407306 0.07902784
202 0.07407306 0.07902784
203 0.07407306 0.07902784
204 0.07407306 0.07902784
209 0.07407306 0.07902784
210 0.07407306 0.07902784
211 0.07407306 0.07902784
212 0.07407306 0.07902784
213 0.07407306 0.07902784
214 0.07407306 0.07902784
217 0.07407306 0.07902784
218 0.07407306 0.07902784
219 0.07407306 0.07902784
220 0.07407306 0.07902784
221 0.07407306 0.07902784
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 0.04188296 -0.04538026
4 0.04188296 -0.04538026
11 0.04188296 -0.04538026
12 0.04188296 -0.04538026
19 0.04188296 -0.04538026
20 0.04188296 -0.04538026
26 0.04188296 -0.04538026
27 0.04188296 -0.04538026
35 0.04188296 -0.04538026
36 0.04188296 -0.04538026
41 0.04188296 -0.04538026
42 0.04188296 -0.04538026
43 0.04188296 -0.04538026
44 0.04188296 -0.04538026
45 0.04188296 -0.04538026
46 0.04188296 -0.04538026
201 0.04188296 -0.04538026
202 0.04188296 -0.04538026
203 0.04188296 -0.04538026
204 0.04188296 -0.04538026
209 0.04188296 -0.04538026
210 0.04188296 -0.04538026
211 0.04188296 -0.04538026
212 0.04188296 -0.04538026
213 0.04188296 -0.04538026
214 0.04188296 -0.04538026
217 0.04188296 -0.04538026
218 0.04188296 -0.04538026
219 0.04188296 -0.04538026
220 0.04188296 -0.04538026
221 0.04188296 -0.04538026
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 -0.1263666 0.07181537
4 -0.1263666 0.07181537
11 -0.1263666 0.07181537
12 -0.1263666 0.07181537
19 -0.1263666 0.07181537
20 -0.1263666 0.07181537
26 -0.1263666 0.07181537
27 -0.1263666 0.07181537
35 -0.1263666 0.07181537
36 -0.1263666 0.07181537
41 -0.1263666 0.07181537
42 -0.1263666 0.07181537
43 -0.1263666 0.07181537
44 -0.1263666 0.07181537
45 -0.1263666 0.07181537
46 -0.1263666 0.07181537
201 -0.1263666 0.07181537
202 -0.1263666 0.07181537
203 -0.1263666 0.07181537
204 -0.1263666 0.07181537
209 -0.1263666 0.07181537
210 -0.1263666 0.07181537
211 -0.1263666 0.07181537
212 -0.1263666 0.07181537
213 -0.1263666 0.07181537
214 -0.1263666 0.07181537
217 -0.1263666 0.07181537
218 -0.1263666 0.07181537
219 -0.1263666 0.07181537
220 -0.1263666 0.07181537
221 -0.1263666 0.07181537
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
prfig2<-ggplot(phys, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
prfig2
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
prfig<-ggplot(phys, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
prfig
library(Rmisc)
PR_sum<-summarySE(phys, measurevar='PR', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedPR_sumPRfig_3<-ggplot(PR_sum, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=PR_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "PR", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=PR-se, ymax=PR+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(Photosynthesis:Respiration), limits=c(0,7))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statPRfig_3
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PR_stress_fig<-ggplot(phys_stress, aes(y=PR, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=PR, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=PR, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PR_stress_fig
library(cowplot)
respall<-cowplot::plot_grid(Pnetfig,LEDRfig, nrow=3,ncol=1, align="h", axis = "bt")Warning: Removed 174 rows containing non-finite values (stat_smooth).Warning: Removed 174 rows containing missing values (geom_point).Warning: Removed 172 rows containing non-finite values (stat_smooth).Warning: Removed 172 rows containing missing values (geom_point).respall
##PI curves
PIOct19<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Oct 2019 PI curve_Teegan.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIOct19$rad<-as.numeric(PIOct19$rad)
PIOct19###Figure - Oct19
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig_Oct19<-ggplot(PIOct19, aes(y=umol.O2.L.hr, x=rad, color=Phenotype, fill=Phenotype))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") +
scale_fill_manual("Phenotype", values=c("Susceptible"= '#DFD3B9',"Resistant"='#796334'))+ #Manually choose the colors
scale_color_manual("Phenotype", values=c("Susceptible"= '#DFD3B9',"Resistant"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfig_Oct19
PIOct<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/2021.10.10_KBaypairs_respirometry/Raw_KTB.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIOct$rad<-as.numeric(PIOct$rad)
PIOct###Figure - Oct21
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig<-ggplot(PIOct, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") +
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig2<-ggplot(PIOct, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+
geom_path()+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfig2
PIMar<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/March 2022 Respirometry/March22_KTB2.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIMar$rad<-as.numeric(PIMar$rad)
PIMar###Figure - Mar22
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfigmarch<-ggplot(PIMar, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") +
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfigmarch
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig2<-ggplot(PIMar, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+
geom_path()+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfig2
PISept<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Sept 2022 Respirometry/Sept2022_slopes_raw.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PISept$rad<-as.numeric(PISept$rad)
PISept$umol.O2.L.hr.cm2<-as.numeric(PISept$umol.O2.L.hr.cm2)Warning: NAs introduced by coercionPISept###Figure - Sept22
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig3<-ggplot(PISept, aes(y=umol.O2.L.hr.cm2, x=rad, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+
scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})),limits=c(-2,3))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") +
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
PIfig3
library(cowplot)
curves<-cowplot::plot_grid(PIfig_Oct19,PIfig,PIfigmarch, PIfig3, nrow=2,ncol=2, align="h", axis = "bt")Warning: Removed 32 rows containing non-finite values (stat_smooth).Warning: Removed 32 rows containing missing values (geom_point).Warning: Removed 9 rows containing non-finite values (stat_smooth).Warning: Removed 9 rows containing missing values (geom_point).curves
##CaCO3 density ###Normality
hist(phys$CaCO3.Density_g.mL.1)
density.lm<- lm(CaCO3.Density_g.mL.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(density.lm, ask=FALSE, which=1:6)
###Stats
density.lme <- lme(CaCO3.Density_g.mL.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(density.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: CaCO3.Density_g.mL.1
Chisq Df Pr(>Chisq)
(Intercept) 354.0711 1 < 2.2e-16 ***
Species 0.0576 1 0.81041
Bleach 0.3358 1 0.56225
Months 113.0932 7 < 2.2e-16 ***
Species:Bleach 0.0075 1 0.93113
Species:Months 31.5586 7 4.903e-05 ***
Bleach:Months 14.1553 7 0.04849 *
Species:Bleach:Months 14.1197 7 0.04909 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(density.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Months")
tukey3$`emmeans of Species, Bleach, Months`
Species Bleach Months emmean SE df lower.CL upper.CL
Montipora capitata Bleach 0 1.38 0.0733 43 1.23 1.53
Porites compressa Bleach 0 1.40 0.0722 42 1.26 1.55
Montipora capitata Non-bleach 0 1.44 0.0733 43 1.29 1.59
Porites compressa Non-bleach 0 1.48 0.0725 42 1.33 1.62
Montipora capitata Bleach 10 2.14 0.0856 43 1.96 2.31
Porites compressa Bleach 10 1.56 0.0800 42 1.40 1.73
Montipora capitata Non-bleach 10 1.93 0.0767 43 1.77 2.08
Porites compressa Non-bleach 10 1.71 0.0755 42 1.55 1.86
Montipora capitata Bleach 12 2.14 0.0733 43 1.99 2.29
Porites compressa Bleach 12 1.64 0.0758 42 1.49 1.79
Montipora capitata Non-bleach 12 2.17 0.0733 43 2.02 2.32
Porites compressa Non-bleach 12 1.49 0.0761 42 1.34 1.65
Montipora capitata Bleach 17 2.11 0.0733 43 1.96 2.26
Porites compressa Bleach 17 1.70 0.0800 42 1.54 1.86
Montipora capitata Non-bleach 17 2.14 0.0733 43 1.99 2.28
Porites compressa Non-bleach 17 1.65 0.0722 42 1.50 1.79
Montipora capitata Bleach 20 1.93 0.0767 43 1.77 2.08
Porites compressa Bleach 20 1.64 0.0758 42 1.49 1.79
Montipora capitata Non-bleach 20 2.06 0.0733 43 1.91 2.21
Porites compressa Non-bleach 20 1.59 0.0761 42 1.43 1.74
Montipora capitata Bleach 24 2.06 0.0768 43 1.91 2.22
Porites compressa Bleach 24 1.54 0.0841 42 1.37 1.71
Montipora capitata Non-bleach 24 1.87 0.0767 43 1.72 2.03
Porites compressa Non-bleach 24 1.52 0.0844 42 1.35 1.69
Montipora capitata Bleach 29 1.97 0.0768 43 1.82 2.13
Porites compressa Bleach 29 1.62 0.0793 42 1.46 1.78
Montipora capitata Non-bleach 29 1.93 0.0767 43 1.78 2.09
Porites compressa Non-bleach 29 1.68 0.0844 42 1.51 1.85
Montipora capitata Bleach 35 1.61 0.1109 43 1.39 1.83
Porites compressa Bleach 35 1.52 0.0850 42 1.35 1.69
Montipora capitata Non-bleach 35 1.85 0.0853 43 1.68 2.02
Porites compressa Non-bleach 35 1.50 0.0988 42 1.30 1.70
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Bleach, Months | Species, Bleach`
Species = Montipora capitata, Bleach = Bleach:
3 estimate SE df t.ratio p.value
Months0 - Months10 -0.75662 0.1005 200 -7.528 <.0001
Months0 - Months12 -0.76172 0.0903 200 -8.437 <.0001
Months0 - Months17 -0.72822 0.0903 200 -8.066 <.0001
Months0 - Months20 -0.54593 0.0930 200 -5.868 <.0001
Months0 - Months24 -0.68299 0.0931 200 -7.336 <.0001
Months0 - Months29 -0.59332 0.0931 200 -6.372 <.0001
Months0 - Months35 -0.23025 0.1250 200 -1.842 0.5920
Months10 - Months12 -0.00510 0.1005 200 -0.051 1.0000
Months10 - Months17 0.02840 0.1005 200 0.283 1.0000
Months10 - Months20 0.21069 0.1032 200 2.041 0.4570
Months10 - Months24 0.07363 0.1024 200 0.719 0.9964
Months10 - Months29 0.16330 0.1024 200 1.595 0.7532
Months10 - Months35 0.52636 0.1326 200 3.970 0.0025
Months12 - Months17 0.03349 0.0903 200 0.371 1.0000
Months12 - Months20 0.21579 0.0930 200 2.319 0.2883
Months12 - Months24 0.07873 0.0931 200 0.846 0.9902
Months12 - Months29 0.16840 0.0931 200 1.809 0.6150
Months12 - Months35 0.53146 0.1250 200 4.253 0.0008
Months17 - Months20 0.18229 0.0930 200 1.959 0.5119
Months17 - Months24 0.04523 0.0931 200 0.486 0.9997
Months17 - Months29 0.13490 0.0931 200 1.449 0.8331
Months17 - Months35 0.49797 0.1250 200 3.985 0.0024
Months20 - Months24 -0.13706 0.0959 200 -1.430 0.8424
Months20 - Months29 -0.04739 0.0959 200 -0.494 0.9997
Months20 - Months35 0.31568 0.1267 200 2.492 0.2048
Months24 - Months29 0.08967 0.0952 200 0.942 0.9815
Months24 - Months35 0.45274 0.1266 200 3.575 0.0102
Months29 - Months35 0.36306 0.1266 200 2.867 0.0850
Species = Porites compressa, Bleach = Bleach:
3 estimate SE df t.ratio p.value
Months0 - Months10 -0.15990 0.0967 200 -1.654 0.7165
Months0 - Months12 -0.23446 0.0934 200 -2.512 0.1966
Months0 - Months17 -0.29232 0.0967 200 -3.024 0.0558
Months0 - Months20 -0.23738 0.0934 200 -2.543 0.1839
Months0 - Months24 -0.13385 0.1014 200 -1.320 0.8903
Months0 - Months29 -0.21942 0.0973 200 -2.256 0.3235
Months0 - Months35 -0.11573 0.1034 200 -1.119 0.9520
Months10 - Months12 -0.07456 0.0984 200 -0.758 0.9950
Months10 - Months17 -0.13242 0.1009 200 -1.312 0.8935
Months10 - Months20 -0.07748 0.0984 200 -0.787 0.9936
Months10 - Months24 0.02605 0.1065 200 0.245 1.0000
Months10 - Months29 -0.05952 0.1024 200 -0.581 0.9991
Months10 - Months35 0.04417 0.1078 200 0.410 0.9999
Months12 - Months17 -0.05786 0.0984 200 -0.588 0.9990
Months12 - Months20 -0.00292 0.0952 200 -0.031 1.0000
Months12 - Months24 0.10061 0.1032 200 0.975 0.9774
Months12 - Months29 0.01504 0.0991 200 0.152 1.0000
Months12 - Months35 0.11873 0.1052 200 1.128 0.9499
Months17 - Months20 0.05494 0.0984 200 0.558 0.9993
Months17 - Months24 0.15847 0.1065 200 1.488 0.8130
Months17 - Months29 0.07290 0.1024 200 0.712 0.9966
Months17 - Months35 0.17659 0.1078 200 1.638 0.7265
Months20 - Months24 0.10353 0.1032 200 1.003 0.9735
Months20 - Months29 0.01796 0.0991 200 0.181 1.0000
Months20 - Months35 0.12165 0.1052 200 1.156 0.9431
Months24 - Months29 -0.08557 0.1048 200 -0.816 0.9921
Months24 - Months35 0.01812 0.1117 200 0.162 1.0000
Months29 - Months35 0.10369 0.1077 200 0.963 0.9790
Species = Montipora capitata, Bleach = Non-bleach:
3 estimate SE df t.ratio p.value
Months0 - Months10 -0.48675 0.0931 200 -5.228 <.0001
Months0 - Months12 -0.73188 0.0903 200 -8.106 <.0001
Months0 - Months17 -0.69585 0.0903 200 -7.707 <.0001
Months0 - Months20 -0.62042 0.0903 200 -6.872 <.0001
Months0 - Months24 -0.43236 0.0931 200 -4.644 0.0002
Months0 - Months29 -0.49325 0.0931 200 -5.298 <.0001
Months0 - Months35 -0.41002 0.1018 200 -4.029 0.0020
Months10 - Months12 -0.24514 0.0931 200 -2.633 0.1504
Months10 - Months17 -0.20911 0.0931 200 -2.246 0.3292
Months10 - Months20 -0.13368 0.0931 200 -1.436 0.8396
Months10 - Months24 0.05438 0.0952 200 0.571 0.9992
Months10 - Months29 -0.00650 0.0952 200 -0.068 1.0000
Months10 - Months35 0.07673 0.1037 200 0.740 0.9957
Months12 - Months17 0.03603 0.0903 200 0.399 0.9999
Months12 - Months20 0.11146 0.0903 200 1.235 0.9207
Months12 - Months24 0.29952 0.0931 200 3.217 0.0320
Months12 - Months29 0.23864 0.0931 200 2.563 0.1759
Months12 - Months35 0.32187 0.1018 200 3.163 0.0375
Months17 - Months20 0.07543 0.0903 200 0.835 0.9909
Months17 - Months24 0.26349 0.0931 200 2.830 0.0935
Months17 - Months29 0.20261 0.0931 200 2.176 0.3707
Months17 - Months35 0.28584 0.1018 200 2.809 0.0986
Months20 - Months24 0.18806 0.0931 200 2.020 0.4712
Months20 - Months29 0.12717 0.0931 200 1.366 0.8715
Months20 - Months35 0.21041 0.1018 200 2.068 0.4395
Months24 - Months29 -0.06089 0.0952 200 -0.640 0.9983
Months24 - Months35 0.02235 0.1037 200 0.215 1.0000
Months29 - Months35 0.08323 0.1037 200 0.802 0.9928
Species = Porites compressa, Bleach = Non-bleach:
3 estimate SE df t.ratio p.value
Months0 - Months10 -0.22972 0.0939 200 -2.447 0.2251
Months0 - Months12 -0.01440 0.0934 200 -0.154 1.0000
Months0 - Months17 -0.16976 0.0911 200 -1.863 0.5777
Months0 - Months20 -0.11074 0.0934 200 -1.186 0.9351
Months0 - Months24 -0.04073 0.1014 200 -0.402 0.9999
Months0 - Months29 -0.20336 0.1014 200 -2.005 0.4808
Months0 - Months35 -0.01911 0.1128 200 -0.169 1.0000
Months10 - Months12 0.21532 0.0958 200 2.248 0.3281
Months10 - Months17 0.05996 0.0930 200 0.644 0.9982
Months10 - Months20 0.11898 0.0958 200 1.242 0.9182
Months10 - Months24 0.18899 0.1039 200 1.820 0.6075
Months10 - Months29 0.02636 0.1039 200 0.254 1.0000
Months10 - Months35 0.21061 0.1143 200 1.843 0.5919
Months12 - Months17 -0.15537 0.0930 200 -1.670 0.7067
Months12 - Months20 -0.09634 0.0952 200 -1.012 0.9722
Months12 - Months24 -0.02633 0.1032 200 -0.255 1.0000
Months12 - Months29 -0.18897 0.1032 200 -1.832 0.5994
Months12 - Months35 -0.00471 0.1143 200 -0.041 1.0000
Months17 - Months20 0.05903 0.0930 200 0.634 0.9984
Months17 - Months24 0.12903 0.1011 200 1.276 0.9066
Months17 - Months29 -0.03360 0.1011 200 -0.332 1.0000
Months17 - Months35 0.15065 0.1125 200 1.339 0.8828
Months20 - Months24 0.07001 0.1032 200 0.679 0.9975
Months20 - Months29 -0.09263 0.1032 200 -0.898 0.9860
Months20 - Months35 0.09163 0.1143 200 0.802 0.9929
Months24 - Months29 -0.16263 0.1087 200 -1.496 0.8087
Months24 - Months35 0.02162 0.1213 200 0.178 1.0000
Months29 - Months35 0.18426 0.1213 200 1.519 0.7967
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 8 estimates summary(density.lme)Linear mixed-effects model fit by REML
Data: phys
Random effects:
Formula: ~1 | Coral_ID
(Intercept) Residual
StdDev: 0.1151611 0.2018896
Fixed effects: CaCO3.Density_g.mL.1 ~ Species * Bleach * Months Correlation:
(Intr) SpcsPc BlchN- Mnth10 Mnth12 Mnth17 Mnth20 Mnth24 Mnth29 Mnth35 SpPc:BN- SPc:M10
SpeciesPorites compressa -0.713
BleachNon-bleach -0.707 0.504
Months10 -0.553 0.394 0.391
Months12 -0.616 0.439 0.435 0.449
Months17 -0.616 0.439 0.435 0.449 0.500
Months20 -0.598 0.426 0.423 0.433 0.485 0.485
Months24 -0.597 0.425 0.422 0.442 0.485 0.485 0.470
Months29 -0.597 0.425 0.422 0.442 0.485 0.485 0.470 0.478
Months35 -0.475 0.338 0.336 0.324 0.361 0.361 0.354 0.355 0.355
SpeciesPorites compressa:BleachNon-bleach 0.507 -0.702 -0.717 -0.280 -0.312 -0.312 -0.303 -0.303 -0.303 -0.241
SpeciesPorites compressa:Months10 0.399 -0.568 -0.282 -0.721 -0.324 -0.324 -0.312 -0.319 -0.319 -0.234 0.404
SpeciesPorites compressa:Months12 0.428 -0.611 -0.303 -0.312 -0.695 -0.348 -0.337 -0.337 -0.337 -0.251 0.435 0.456
SpeciesPorites compressa:Months17 0.420 -0.599 -0.297 -0.307 -0.341 -0.683 -0.331 -0.331 -0.331 -0.247 0.426 0.451
SpeciesPorites compressa:Months20 0.422 -0.602 -0.298 -0.306 -0.343 -0.343 -0.706 -0.332 -0.332 -0.250 0.429 0.448
SpeciesPorites compressa:Months24 0.404 -0.585 -0.286 -0.299 -0.328 -0.328 -0.318 -0.676 -0.323 -0.240 0.423 0.432
SpeciesPorites compressa:Months29 0.413 -0.597 -0.292 -0.306 -0.335 -0.335 -0.325 -0.330 -0.691 -0.245 0.430 0.442
SpeciesPorites compressa:Months35 0.366 -0.520 -0.259 -0.250 -0.278 -0.278 -0.273 -0.273 -0.273 -0.770 0.368 0.366
BleachNon-bleach:Months10 0.406 -0.289 -0.574 -0.734 -0.330 -0.330 -0.318 -0.325 -0.325 -0.238 0.411 0.529
BleachNon-bleach:Months12 0.435 -0.310 -0.616 -0.318 -0.707 -0.354 -0.343 -0.343 -0.343 -0.255 0.441 0.229
BleachNon-bleach:Months17 0.435 -0.310 -0.616 -0.318 -0.354 -0.707 -0.343 -0.343 -0.343 -0.255 0.441 0.229
BleachNon-bleach:Months20 0.429 -0.306 -0.607 -0.311 -0.348 -0.348 -0.718 -0.337 -0.337 -0.254 0.435 0.224
BleachNon-bleach:Months24 0.422 -0.301 -0.597 -0.313 -0.343 -0.343 -0.332 -0.707 -0.338 -0.251 0.428 0.226
BleachNon-bleach:Months29 0.422 -0.301 -0.597 -0.313 -0.343 -0.343 -0.332 -0.338 -0.707 -0.251 0.428 0.226
BleachNon-bleach:Months35 0.368 -0.262 -0.513 -0.251 -0.280 -0.280 -0.274 -0.275 -0.275 -0.775 0.368 0.181
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.289 0.417 0.409 0.522 0.235 0.235 0.226 0.231 0.231 0.169 -0.593 -0.726
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.303 0.433 0.428 0.221 0.492 0.246 0.239 0.238 0.238 0.178 -0.616 -0.323
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.301 0.434 0.426 0.220 0.245 0.489 0.238 0.237 0.237 0.177 -0.618 -0.325
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.300 0.430 0.425 0.218 0.244 0.244 0.503 0.236 0.236 0.178 -0.611 -0.319
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.285 0.419 0.403 0.211 0.231 0.231 0.224 0.477 0.228 0.169 -0.596 -0.303
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.288 0.422 0.407 0.213 0.234 0.234 0.226 0.230 0.482 0.171 -0.601 -0.307
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.267 0.381 0.372 0.182 0.203 0.203 0.199 0.199 0.199 0.562 -0.529 -0.267
SPc:M12 SPc:M17 SPc:M20 SPc:M24 SPc:M29 SPc:M3 BN-:M10 BN-:M12 BN-:M17 BN-:M20 BN-:M24
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17 0.481
SpeciesPorites compressa:Months20 0.483 0.474
SpeciesPorites compressa:Months24 0.462 0.451 0.454
SpeciesPorites compressa:Months29 0.472 0.462 0.465 0.459
SpeciesPorites compressa:Months35 0.391 0.386 0.387 0.375 0.385
BleachNon-bleach:Months10 0.229 0.225 0.224 0.220 0.224 0.183
BleachNon-bleach:Months12 0.492 0.241 0.242 0.232 0.237 0.197 0.466
BleachNon-bleach:Months17 0.246 0.483 0.242 0.232 0.237 0.197 0.466 0.500
BleachNon-bleach:Months20 0.242 0.238 0.507 0.228 0.233 0.196 0.458 0.492 0.492
BleachNon-bleach:Months24 0.238 0.234 0.234 0.478 0.234 0.193 0.459 0.485 0.485 0.477
BleachNon-bleach:Months29 0.238 0.234 0.234 0.228 0.489 0.193 0.459 0.485 0.485 0.477 0.478
BleachNon-bleach:Months35 0.195 0.191 0.194 0.186 0.190 0.597 0.371 0.396 0.396 0.392 0.389
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.330 -0.329 -0.325 -0.312 -0.320 -0.267 -0.712 -0.332 -0.332 -0.326 -0.327
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.707 -0.340 -0.341 -0.326 -0.333 -0.277 -0.324 -0.695 -0.348 -0.342 -0.337
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.345 -0.719 -0.340 -0.323 -0.331 -0.278 -0.323 -0.346 -0.692 -0.341 -0.336
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.344 -0.338 -0.712 -0.323 -0.331 -0.276 -0.321 -0.345 -0.345 -0.701 -0.334
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.325 -0.317 -0.320 -0.709 -0.328 -0.267 -0.309 -0.327 -0.327 -0.322 -0.674
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.329 -0.321 -0.323 -0.325 -0.702 -0.271 -0.313 -0.330 -0.330 -0.325 -0.326
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.285 -0.282 -0.283 -0.272 -0.279 -0.730 -0.269 -0.287 -0.287 -0.284 -0.282
BN-:M29 BN-:M3 SPc:BN-:M10 SPc:BN-:M12 SPc:BN-:M17 SPc:BN-:M20 SPc:BN-:M24 SPc:BN-:M29
SpeciesPorites compressa
BleachNon-bleach
Months10
Months12
Months17
Months20
Months24
Months29
Months35
SpeciesPorites compressa:BleachNon-bleach
SpeciesPorites compressa:Months10
SpeciesPorites compressa:Months12
SpeciesPorites compressa:Months17
SpeciesPorites compressa:Months20
SpeciesPorites compressa:Months24
SpeciesPorites compressa:Months29
SpeciesPorites compressa:Months35
BleachNon-bleach:Months10
BleachNon-bleach:Months12
BleachNon-bleach:Months17
BleachNon-bleach:Months20
BleachNon-bleach:Months24
BleachNon-bleach:Months29
BleachNon-bleach:Months35 0.389
SpeciesPorites compressa:BleachNon-bleach:Months10 -0.327 -0.265
SpeciesPorites compressa:BleachNon-bleach:Months12 -0.337 -0.275 0.467
SpeciesPorites compressa:BleachNon-bleach:Months17 -0.336 -0.274 0.471 0.487
SpeciesPorites compressa:BleachNon-bleach:Months20 -0.334 -0.275 0.463 0.486 0.484
SpeciesPorites compressa:BleachNon-bleach:Months24 -0.322 -0.262 0.440 0.459 0.456 0.456
SpeciesPorites compressa:BleachNon-bleach:Months29 -0.682 -0.265 0.445 0.465 0.462 0.461 0.458
SpeciesPorites compressa:BleachNon-bleach:Months35 -0.282 -0.725 0.391 0.404 0.405 0.402 0.384 0.389
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.90790710 -0.50056191 0.01416292 0.49627526 5.44311100
Number of Observations: 274
Number of Groups: 44 r.squaredGLMM(density.lme) R2m R2c
[1,] 0.5472388 0.6583901####Coefficients
coef(density.lme) (Intercept) SpeciesPorites compressa BleachNon-bleach Months10 Months12 Months17 Months20 Months24 Months29 Months35
3 1.422854 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
4 1.496050 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
11 1.479152 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
12 1.368736 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
19 1.259597 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
20 1.403027 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
26 1.355956 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
27 1.404411 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
35 1.406561 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
36 1.414745 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
41 1.278309 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
42 1.266362 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
43 1.487963 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
44 1.407813 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
45 1.449593 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
46 1.434104 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
201 1.448446 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
202 1.416723 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
203 1.340943 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
204 1.523062 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
209 1.347887 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
210 1.321702 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
211 1.476658 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
212 1.475596 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
213 1.432124 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
214 1.465690 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
217 1.455229 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
218 1.268534 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
219 1.188597 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
220 1.253742 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
221 1.326277 0.02468911 0.06008718 0.7566164 0.7617162 0.7282214 0.5459274 0.6829894 0.5933164 0.2302514
SpeciesPorites compressa:BleachNon-bleach SpeciesPorites compressa:Months10 SpeciesPorites compressa:Months12
3 0.012503 -0.5967163 -0.5272567
4 0.012503 -0.5967163 -0.5272567
11 0.012503 -0.5967163 -0.5272567
12 0.012503 -0.5967163 -0.5272567
19 0.012503 -0.5967163 -0.5272567
20 0.012503 -0.5967163 -0.5272567
26 0.012503 -0.5967163 -0.5272567
27 0.012503 -0.5967163 -0.5272567
35 0.012503 -0.5967163 -0.5272567
36 0.012503 -0.5967163 -0.5272567
41 0.012503 -0.5967163 -0.5272567
42 0.012503 -0.5967163 -0.5272567
43 0.012503 -0.5967163 -0.5272567
44 0.012503 -0.5967163 -0.5272567
45 0.012503 -0.5967163 -0.5272567
46 0.012503 -0.5967163 -0.5272567
201 0.012503 -0.5967163 -0.5272567
202 0.012503 -0.5967163 -0.5272567
203 0.012503 -0.5967163 -0.5272567
204 0.012503 -0.5967163 -0.5272567
209 0.012503 -0.5967163 -0.5272567
210 0.012503 -0.5967163 -0.5272567
211 0.012503 -0.5967163 -0.5272567
212 0.012503 -0.5967163 -0.5272567
213 0.012503 -0.5967163 -0.5272567
214 0.012503 -0.5967163 -0.5272567
217 0.012503 -0.5967163 -0.5272567
218 0.012503 -0.5967163 -0.5272567
219 0.012503 -0.5967163 -0.5272567
220 0.012503 -0.5967163 -0.5272567
221 0.012503 -0.5967163 -0.5272567
SpeciesPorites compressa:Months17 SpeciesPorites compressa:Months20 SpeciesPorites compressa:Months24 SpeciesPorites compressa:Months29
3 -0.4359007 -0.3085493 -0.5491413 -0.3738975
4 -0.4359007 -0.3085493 -0.5491413 -0.3738975
11 -0.4359007 -0.3085493 -0.5491413 -0.3738975
12 -0.4359007 -0.3085493 -0.5491413 -0.3738975
19 -0.4359007 -0.3085493 -0.5491413 -0.3738975
20 -0.4359007 -0.3085493 -0.5491413 -0.3738975
26 -0.4359007 -0.3085493 -0.5491413 -0.3738975
27 -0.4359007 -0.3085493 -0.5491413 -0.3738975
35 -0.4359007 -0.3085493 -0.5491413 -0.3738975
36 -0.4359007 -0.3085493 -0.5491413 -0.3738975
41 -0.4359007 -0.3085493 -0.5491413 -0.3738975
42 -0.4359007 -0.3085493 -0.5491413 -0.3738975
43 -0.4359007 -0.3085493 -0.5491413 -0.3738975
44 -0.4359007 -0.3085493 -0.5491413 -0.3738975
45 -0.4359007 -0.3085493 -0.5491413 -0.3738975
46 -0.4359007 -0.3085493 -0.5491413 -0.3738975
201 -0.4359007 -0.3085493 -0.5491413 -0.3738975
202 -0.4359007 -0.3085493 -0.5491413 -0.3738975
203 -0.4359007 -0.3085493 -0.5491413 -0.3738975
204 -0.4359007 -0.3085493 -0.5491413 -0.3738975
209 -0.4359007 -0.3085493 -0.5491413 -0.3738975
210 -0.4359007 -0.3085493 -0.5491413 -0.3738975
211 -0.4359007 -0.3085493 -0.5491413 -0.3738975
212 -0.4359007 -0.3085493 -0.5491413 -0.3738975
213 -0.4359007 -0.3085493 -0.5491413 -0.3738975
214 -0.4359007 -0.3085493 -0.5491413 -0.3738975
217 -0.4359007 -0.3085493 -0.5491413 -0.3738975
218 -0.4359007 -0.3085493 -0.5491413 -0.3738975
219 -0.4359007 -0.3085493 -0.5491413 -0.3738975
220 -0.4359007 -0.3085493 -0.5491413 -0.3738975
221 -0.4359007 -0.3085493 -0.5491413 -0.3738975
SpeciesPorites compressa:Months35 BleachNon-bleach:Months10 BleachNon-bleach:Months12 BleachNon-bleach:Months17 BleachNon-bleach:Months20
3 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
4 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
11 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
12 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
19 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
20 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
26 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
27 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
35 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
36 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
41 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
42 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
43 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
44 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
45 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
46 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
201 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
202 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
203 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
204 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
209 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
210 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
211 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
212 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
213 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
214 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
217 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
218 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
219 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
220 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
221 -0.1145251 -0.2698704 -0.02983298 -0.03236749 0.07449399
BleachNon-bleach:Months24 BleachNon-bleach:Months29 BleachNon-bleach:Months35 SpeciesPorites compressa:BleachNon-bleach:Months10
3 -0.2506278 -0.1000698 0.1797646 0.3396912
4 -0.2506278 -0.1000698 0.1797646 0.3396912
11 -0.2506278 -0.1000698 0.1797646 0.3396912
12 -0.2506278 -0.1000698 0.1797646 0.3396912
19 -0.2506278 -0.1000698 0.1797646 0.3396912
20 -0.2506278 -0.1000698 0.1797646 0.3396912
26 -0.2506278 -0.1000698 0.1797646 0.3396912
27 -0.2506278 -0.1000698 0.1797646 0.3396912
35 -0.2506278 -0.1000698 0.1797646 0.3396912
36 -0.2506278 -0.1000698 0.1797646 0.3396912
41 -0.2506278 -0.1000698 0.1797646 0.3396912
42 -0.2506278 -0.1000698 0.1797646 0.3396912
43 -0.2506278 -0.1000698 0.1797646 0.3396912
44 -0.2506278 -0.1000698 0.1797646 0.3396912
45 -0.2506278 -0.1000698 0.1797646 0.3396912
46 -0.2506278 -0.1000698 0.1797646 0.3396912
201 -0.2506278 -0.1000698 0.1797646 0.3396912
202 -0.2506278 -0.1000698 0.1797646 0.3396912
203 -0.2506278 -0.1000698 0.1797646 0.3396912
204 -0.2506278 -0.1000698 0.1797646 0.3396912
209 -0.2506278 -0.1000698 0.1797646 0.3396912
210 -0.2506278 -0.1000698 0.1797646 0.3396912
211 -0.2506278 -0.1000698 0.1797646 0.3396912
212 -0.2506278 -0.1000698 0.1797646 0.3396912
213 -0.2506278 -0.1000698 0.1797646 0.3396912
214 -0.2506278 -0.1000698 0.1797646 0.3396912
217 -0.2506278 -0.1000698 0.1797646 0.3396912
218 -0.2506278 -0.1000698 0.1797646 0.3396912
219 -0.2506278 -0.1000698 0.1797646 0.3396912
220 -0.2506278 -0.1000698 0.1797646 0.3396912
221 -0.2506278 -0.1000698 0.1797646 0.3396912
SpeciesPorites compressa:BleachNon-bleach:Months12 SpeciesPorites compressa:BleachNon-bleach:Months17
3 -0.1902288 -0.09019032
4 -0.1902288 -0.09019032
11 -0.1902288 -0.09019032
12 -0.1902288 -0.09019032
19 -0.1902288 -0.09019032
20 -0.1902288 -0.09019032
26 -0.1902288 -0.09019032
27 -0.1902288 -0.09019032
35 -0.1902288 -0.09019032
36 -0.1902288 -0.09019032
41 -0.1902288 -0.09019032
42 -0.1902288 -0.09019032
43 -0.1902288 -0.09019032
44 -0.1902288 -0.09019032
45 -0.1902288 -0.09019032
46 -0.1902288 -0.09019032
201 -0.1902288 -0.09019032
202 -0.1902288 -0.09019032
203 -0.1902288 -0.09019032
204 -0.1902288 -0.09019032
209 -0.1902288 -0.09019032
210 -0.1902288 -0.09019032
211 -0.1902288 -0.09019032
212 -0.1902288 -0.09019032
213 -0.1902288 -0.09019032
214 -0.1902288 -0.09019032
217 -0.1902288 -0.09019032
218 -0.1902288 -0.09019032
219 -0.1902288 -0.09019032
220 -0.1902288 -0.09019032
221 -0.1902288 -0.09019032
SpeciesPorites compressa:BleachNon-bleach:Months20 SpeciesPorites compressa:BleachNon-bleach:Months24
3 -0.2011351 0.1575106
4 -0.2011351 0.1575106
11 -0.2011351 0.1575106
12 -0.2011351 0.1575106
19 -0.2011351 0.1575106
20 -0.2011351 0.1575106
26 -0.2011351 0.1575106
27 -0.2011351 0.1575106
35 -0.2011351 0.1575106
36 -0.2011351 0.1575106
41 -0.2011351 0.1575106
42 -0.2011351 0.1575106
43 -0.2011351 0.1575106
44 -0.2011351 0.1575106
45 -0.2011351 0.1575106
46 -0.2011351 0.1575106
201 -0.2011351 0.1575106
202 -0.2011351 0.1575106
203 -0.2011351 0.1575106
204 -0.2011351 0.1575106
209 -0.2011351 0.1575106
210 -0.2011351 0.1575106
211 -0.2011351 0.1575106
212 -0.2011351 0.1575106
213 -0.2011351 0.1575106
214 -0.2011351 0.1575106
217 -0.2011351 0.1575106
218 -0.2011351 0.1575106
219 -0.2011351 0.1575106
220 -0.2011351 0.1575106
221 -0.2011351 0.1575106
SpeciesPorites compressa:BleachNon-bleach:Months29 SpeciesPorites compressa:BleachNon-bleach:Months35
3 0.08401511 -0.2763828
4 0.08401511 -0.2763828
11 0.08401511 -0.2763828
12 0.08401511 -0.2763828
19 0.08401511 -0.2763828
20 0.08401511 -0.2763828
26 0.08401511 -0.2763828
27 0.08401511 -0.2763828
35 0.08401511 -0.2763828
36 0.08401511 -0.2763828
41 0.08401511 -0.2763828
42 0.08401511 -0.2763828
43 0.08401511 -0.2763828
44 0.08401511 -0.2763828
45 0.08401511 -0.2763828
46 0.08401511 -0.2763828
201 0.08401511 -0.2763828
202 0.08401511 -0.2763828
203 0.08401511 -0.2763828
204 0.08401511 -0.2763828
209 0.08401511 -0.2763828
210 0.08401511 -0.2763828
211 0.08401511 -0.2763828
212 0.08401511 -0.2763828
213 0.08401511 -0.2763828
214 0.08401511 -0.2763828
217 0.08401511 -0.2763828
218 0.08401511 -0.2763828
219 0.08401511 -0.2763828
220 0.08401511 -0.2763828
221 0.08401511 -0.2763828
[ reached 'max' / getOption("max.print") -- omitted 13 rows ]###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
densityfig<-ggplot(phys, aes(y=CaCO3.Density_g.mL.1, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1,2.5))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
densityfig
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
density_stress_fig<-ggplot(phys_stress, aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach, fill=Bleach))+
geom_point(data=phys_stress,aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
geom_boxplot(data=phys_stress,aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
geom_boxplot( alpha=0.6, outlier.shape = NA, color="black")+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1,2.5))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
density_stress_fig
library(Rmisc)
density_sum<-summarySE(phys, measurevar='CaCO3.Density_g.mL.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
density_sumdensityfig_3<-ggplot(density_sum, aes(y=CaCO3.Density_g.mL.1, x=Date, color=Bleach, fill=Bleach))+
geom_point(size=1, position=position_dodge(0.3),stat="identity")+
#geom_point(data=phys, aes(y=density_mg.cm.2, x=Date), alpha=0.4)+
#geom_smooth(method="gam", formula = y ~ s(x, bs = "density", k=3), se=F)+
facet_wrap(~Species)+
geom_linerange(aes(ymin=CaCO3.Density_g.mL.1-se, ymax=CaCO3.Density_g.mL.1+se), width= 0.7, position=position_dodge(0.3),stat="identity") +
geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+
scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1.2,2.2))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12,face="italic"))Warning: Ignoring unknown parameters: widthWarning: Ignoring unknown aesthetics: statdensityfig_3
##Internal volume ###Normality
hist(phys$X.internal.volume)
intvol.lm<- lm(X.internal.volume~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(intvol.lm, ask=FALSE, which=1:6)
###Stats
intvol.lme <- lme(X.internal.volume~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(intvol.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: X.internal.volume
Chisq Df Pr(>Chisq)
(Intercept) 195.1880 1 < 2.2e-16 ***
Species 0.2671 1 0.605317
Bleach 1.5242 1 0.216988
Months 103.2891 7 < 2.2e-16 ***
Species:Bleach 0.0245 1 0.875526
Species:Months 26.4123 7 0.000425 ***
Bleach:Months 13.8235 7 0.054411 .
Species:Bleach:Months 10.9181 7 0.142232
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(intvol.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Bleach")
tukey3$`emmeans of Species, Bleach, Months`
Species Bleach Months emmean SE df lower.CL upper.CL
Montipora capitata Bleach 0 34.4 2.46 43 29.4 39.4
Porites compressa Bleach 0 32.6 2.44 42 27.7 37.5
Montipora capitata Non-bleach 0 38.7 2.46 43 33.7 43.6
Porites compressa Non-bleach 0 37.7 2.44 42 32.7 42.6
Montipora capitata Bleach 10 58.4 2.89 43 52.6 64.2
Porites compressa Bleach 10 40.8 2.71 42 35.3 46.2
Montipora capitata Non-bleach 10 54.7 2.58 43 49.5 60.0
Porites compressa Non-bleach 10 45.3 2.55 42 40.2 50.5
Montipora capitata Bleach 12 59.8 2.46 43 54.9 64.8
Porites compressa Bleach 12 41.2 2.56 42 36.1 46.4
Montipora capitata Non-bleach 12 57.6 2.46 43 52.7 62.6
Porites compressa Non-bleach 12 35.9 2.57 42 30.8 41.1
Montipora capitata Bleach 17 57.6 2.46 43 52.6 62.5
Porites compressa Bleach 17 44.9 2.71 42 39.4 50.4
Montipora capitata Non-bleach 17 57.6 2.46 43 52.6 62.5
Porites compressa Non-bleach 17 41.3 2.43 42 36.4 46.2
Montipora capitata Bleach 20 52.5 2.58 43 47.3 57.7
Porites compressa Bleach 20 40.8 2.56 42 35.7 46.0
Montipora capitata Non-bleach 20 55.9 2.46 43 51.0 60.9
Porites compressa Non-bleach 20 39.8 2.57 42 34.6 45.0
Montipora capitata Bleach 24 57.8 2.58 43 52.6 63.0
Porites compressa Bleach 24 36.6 2.85 42 30.8 42.4
Montipora capitata Non-bleach 24 49.9 2.58 43 44.7 55.1
Porites compressa Non-bleach 24 36.5 2.86 42 30.8 42.3
Montipora capitata Bleach 29 54.2 2.58 43 49.0 59.4
Porites compressa Bleach 29 41.3 2.69 42 35.9 46.7
Montipora capitata Non-bleach 29 52.8 2.58 43 47.6 58.0
Porites compressa Non-bleach 29 43.5 2.86 42 37.7 49.3
Montipora capitata Bleach 35 41.8 3.76 43 34.2 49.4
Porites compressa Bleach 35 37.2 2.88 42 31.4 43.0
Montipora capitata Non-bleach 35 50.2 2.88 43 44.4 56.0
Porites compressa Non-bleach 35 34.5 3.36 42 27.8 41.3
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Bleach, Months | Species, Months`
Species = Montipora capitata, Months = 0:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -4.29699 3.48 200 -1.235 0.2184
Species = Porites compressa, Months = 0:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -5.06079 3.41 200 -1.482 0.1399
Species = Montipora capitata, Months = 10:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 3.66757 3.87 200 0.947 0.3449
Species = Porites compressa, Months = 10:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -4.57267 3.67 200 -1.245 0.2146
Species = Montipora capitata, Months = 12:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 2.22188 3.48 200 0.638 0.5240
Species = Porites compressa, Months = 12:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 5.27971 3.59 200 1.472 0.1426
Species = Montipora capitata, Months = 17:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 0.00174 3.48 200 0.001 0.9996
Species = Porites compressa, Months = 17:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 3.56264 3.59 200 0.991 0.3229
Species = Montipora capitata, Months = 20:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -3.44168 3.56 200 -0.966 0.3354
Species = Porites compressa, Months = 20:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 1.04210 3.59 200 0.291 0.7717
Species = Montipora capitata, Months = 24:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 7.82706 3.65 200 2.145 0.0332
Species = Porites compressa, Months = 24:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 0.06105 3.98 200 0.015 0.9878
Species = Montipora capitata, Months = 29:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 1.38897 3.65 200 0.381 0.7039
Species = Porites compressa, Months = 29:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -2.17047 3.87 200 -0.561 0.5752
Species = Montipora capitata, Months = 35:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -8.45866 4.74 200 -1.785 0.0758
Species = Porites compressa, Months = 35:
3 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 2.65122 4.40 200 0.602 0.5476
Degrees-of-freedom method: containment ###Figure
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
intvolfig<-ggplot(phys, aes(y=X.internal.volume, x=Date, color=Bleach, fill=Bleach))+
geom_point(alpha=0.4)+
geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
#geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7, outlier.shape = NA)+
facet_grid(~Species)+
scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
scale_y_continuous(expression(Internal~volume~("%")))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
intvolfig
library(cowplot)
allphys<-cowplot::plot_grid(proteinfig_3,lipidfig_3,AFDWfig_3,densityfig_3,ppofig_3,melfig_3, symfig_3,chlafig_3,chlacellfig_3, Pnetfig_3, LEDRfig_3,PRfig_3,nrow=4, ncol=3, align="h", axis = "bt")Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_segment).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 11 rows containing missing values (geom_segment).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 8 rows containing missing values (geom_segment).allphys
library(cowplot)
allphyssupp<-cowplot::plot_grid(tacfig_3,csfig_3,ppofig_3,melfig_3, chlacellfig_3,tacfig_3,csfig_3,ppofig_3,melfig_3, chlacellfig_3,melfig_3, chlacellfig_3,nrow=4, ncol=3, align="h", axis = "bt")Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 2 rows containing missing values (geom_segment).Warning: Removed 3 rows containing missing values (geom_segment).Warning: Removed 2 row(s) containing missing values (geom_path).allphyssupp
library(cowplot)
phys2<-plot_grid(proteinfig,symfig, nrow=2, ncol=1, align="h", axis = "bt")Error in plot_grid(proteinfig, symfig, nrow = 2, ncol = 1, align = "h", :
unused arguments (nrow = 2, ncol = 1, align = "h", axis = "bt")#Composite Figure
library(cowplot)
allphys_stress<-cowplot::plot_grid(AFDW_stress_fig,protein_stress_fig,lipid_stress_fig, density_stress_fig,sym_stress_fig,chla_stress_fig,tac_stress_fig,mel_stress_fig,ppo_stress_fig,pnet_stress_fig,LEDR_stress_fig,PR_stress_fig, nrow=4, ncol=3, align="h", axis = "bt")Warning: Removed 41 rows containing non-finite values (stat_boxplot).Warning: Removed 41 rows containing missing values (geom_point).Warning: Removed 40 rows containing non-finite values (stat_boxplot).Warning: Removed 40 rows containing missing values (geom_point).Warning: Removed 85 rows containing non-finite values (stat_boxplot).Warning: Removed 85 rows containing missing values (geom_point).Warning: Removed 40 rows containing non-finite values (stat_boxplot).Warning: Removed 40 rows containing non-finite values (stat_boxplot).Warning: Removed 40 rows containing missing values (geom_point).Warning: Removed 41 rows containing non-finite values (stat_boxplot).Warning: Removed 41 rows containing non-finite values (stat_boxplot).Warning: Removed 41 rows containing missing values (geom_point).Warning: Removed 40 rows containing non-finite values (stat_boxplot).Warning: Removed 40 rows containing non-finite values (stat_boxplot).Warning: Removed 40 rows containing missing values (geom_point).Warning: Removed 63 rows containing non-finite values (stat_boxplot).Warning: Removed 63 rows containing missing values (geom_point).Warning: Removed 83 rows containing non-finite values (stat_boxplot).Warning: Removed 83 rows containing non-finite values (stat_boxplot).Warning: Removed 83 rows containing missing values (geom_point).Warning: Removed 81 rows containing non-finite values (stat_boxplot).Warning: Removed 81 rows containing non-finite values (stat_boxplot).Warning: Removed 81 rows containing missing values (geom_point).Warning: Removed 63 rows containing non-finite values (stat_boxplot).Warning: Removed 63 rows containing missing values (geom_point).Warning: Removed 61 rows containing non-finite values (stat_boxplot).Warning: Removed 61 rows containing missing values (geom_point).Warning: Removed 64 rows containing non-finite values (stat_boxplot).Warning: Removed 64 rows containing missing values (geom_point).allphys_stress
library(cowplot)
allphys_stress<-cowplot::plot_grid(proteinfig,AFDWfig,lipidfig,densityfig,symfig,chlafig,tacfig,ppofig,csfig,Pnetfig_3,LEDRfig_3,PRfig_3, nrow=4, ncol=3, align="h", axis = "bt")Warning: Removed 40 rows containing non-finite values (stat_smooth).Warning: Removed 40 rows containing missing values (geom_point).Warning: Removed 41 rows containing non-finite values (stat_smooth).Warning: Removed 41 rows containing missing values (geom_point).Warning: Removed 87 rows containing non-finite values (stat_smooth).Warning: Removed 87 rows containing missing values (geom_point).Warning: Removed 43 rows containing non-finite values (stat_smooth).Warning: Removed 43 rows containing missing values (geom_point).Warning: Removed 45 rows containing non-finite values (stat_smooth).Warning: Removed 45 rows containing missing values (geom_point).Warning: Removed 40 rows containing non-finite values (stat_smooth).Warning: Removed 40 rows containing missing values (geom_point).Warning: Removed 63 rows containing non-finite values (stat_smooth).Warning: Removed 63 rows containing missing values (geom_point).Warning: Removed 83 rows containing non-finite values (stat_smooth).Warning: Removed 83 rows containing missing values (geom_point).Warning: Removed 80 rows containing non-finite values (stat_smooth).Warning: Removed 80 rows containing missing values (geom_point).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 11 rows containing missing values (geom_segment).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 16 rows containing missing values (geom_point).Warning: Removed 8 rows containing missing values (geom_segment).Warning: Removed 8 rows containing missing values (geom_segment).allphys_stress
##Multivariate
phys<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Phys data with Teegan MDS no Oct-Nov 2020 and only peak heatwave.csv", strip.white=T)Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d hh:mm:ss'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d hh:mm:ss'phys$Date<- as.Date(phys$Date, format = "%Y-%m-%d")
phys$Bleach<-as.factor(phys$Bleach)
phys$Months<-as.factor(phys$Months)
phys$Coral<-as.factor(phys$Coral)
phys$Coral_ID<-as.factor(phys$Coral_ID)
physlibrary(lubridate)
library(dplyr)
#grouping each June-March; Jan-Mar "recovery"; June to June calendar year; heat stress (date when it falls below MMM) define this as recovery; bleaching remains Jan/Feb
phys$day <- day(as.POSIXlt(phys$Date))
phys$month <- month(as.POSIXlt(phys$Date))
phys$year <- year(as.POSIXlt(phys$Date))
phys$year<-as.factor(phys$year)
phys<-phys%>%
mutate(season= ifelse (month %in% c(5,6,7,8,9,10), "summer",
ifelse(month %in% c(11,12,1,2,3,4), "winter", NA))) %>%
mutate(period= ifelse(year %in% c(2019) & month %in% c(9,10,11,12), "A",
ifelse(year %in% c(2019) & month %in% c(5,6,7,8), "A",
ifelse(year %in% c(2020) & month %in% c(1,2,3,4), "A",
ifelse(year %in% c(2020) & month %in% c(5,6,7,8,9,10,11,12), "B",
ifelse(year %in% c(2021) & month %in% c(1,2,3,4), "B",
ifelse(year %in% c(2021) & month %in% c(5,6,7,8,9,10,11,12),"C",
ifelse(year %in% c(2022) & month %in% c(1,2,3,4), "C",NA))))))))
phys#phys<-filter(phys, Period == c("Recovery"))
#physunique(phys$Period)[1] "Recovery" "Heatwave"colnames(phys) [1] "Coral_ID" "Coral" "Bleach" "Date" "Period"
[6] "Months" "Protein_mg.cm.2" "Sym.density_10.6cells.cm.2" "Chl.a_ug.cm2" "CaCO3.Density_g.mL.1"
[11] "X.internal.volume" "pg.Chl.a.per.zoox" "AFDW_mg.cm.2" "TAC_CRE.mgprotein.1" "ug.Chl.a.per.zoox"
[16] "day" "month" "year" "season" "period" library(vegan)Warning: package ‘vegan’ was built under R version 4.0.5Loading required package: permute
Warning: package ‘permute’ was built under R version 4.0.5This is vegan 2.6-2phys.rda<- rda(phys[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)biplot(phys.rda, scaling=1, main='Scaling')
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, phys)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scoresinclude_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]g<-ggplot()+
geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
facet_wrap(~Coral)+
geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
scale_color_brewer(palette = "RdYlBu")+
#scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors
scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
g
library(cowplot)
pcaillustrator<-cowplot::plot_grid(g,g,g, nrow=3, align="h", axis = "bt")
pcaillustrator
eig<-eigenvals(phys.rda)
eig PC1 PC2 PC3 PC4 PC5 PC6 PC7
3.418037 1.809117 0.884431 0.435066 0.282408 0.134055 0.036887 veg.hull= pca.sites.scores %>% group_by(Months) %>%
do({
x=.
x[chull(x$PC1, x$PC2),]
})g+ geom_polygon(data=veg.hull, aes(y=PC2, x=PC1,fill=Months), alpha=0.2)+
scale_fill_brewer(palette = "RdYlBu")
###MDS Montipora only
mdsmon<-dplyr::filter(phys, Coral== c("Montipora capitata"))
colnames(mdsmon) [1] "Coral_ID" "Coral" "Bleach" "Date" "Period"
[6] "Months" "Protein_mg.cm.2" "Sym.density_10.6cells.cm.2" "Chl.a_ug.cm2" "CaCO3.Density_g.mL.1"
[11] "X.internal.volume" "pg.Chl.a.per.zoox" "AFDW_mg.cm.2" "TAC_CRE.mgprotein.1" "ug.Chl.a.per.zoox"
[16] "day" "month" "year" "season" "period" #row.has.na <- apply(mdsbefore[,(8:17)], 1, function(x){any(is.na(x))})
#mdsbefore.filtered <- mdsbefore[!row.has.na,]
#mdsbefore.filteredlibrary(vegan)
phys.rda<- rda(mdsmon[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)biplot(phys.rda, scaling=1, main='Scaling')
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, mdsmon)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scoresinclude_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]gmon<-ggplot()+
geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
facet_wrap(~Coral)+
geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
scale_color_brewer(palette = "RdYlBu")+
#scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors
scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
gmon
gmonseason<-ggplot()+
geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=season, shape=Bleach), size=3, alpha=0.8)+
facet_wrap(~Coral)+
geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
#scale_color_brewer(palette = "RdYlBu")+
scale_color_manual("season", values=c("summer"='indianred3', "winter"= "navyblue","NA"="white"))+
#scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors
scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
gmonseason
library(cowplot)
pcaillustrator<-cowplot::plot_grid(gmon,gpor,gmonseason, gporseason, nrow=2, align="h", axis = "bt")Error in cowplot::plot_grid(gmon, gpor, gmonseason, gporseason, nrow = 2, :
object 'gpor' not foundeig<-eigenvals(phys.rda)
eig PC1 PC2 PC3 PC4 PC5 PC6 PC7
2.7269852 1.7135592 1.4518895 0.4752762 0.3634977 0.2196260 0.0491662 veg.hull= pca.sites.scores %>% group_by(Months) %>%
do({
x=.
x[chull(x$PC1, x$PC2),]
})###MDS Porites only
mdspor<-dplyr::filter(phys, Coral== c("Porites compressa"))
colnames(mdspor) [1] "Coral_ID" "Coral" "Bleach" "Date" "Period"
[6] "Months" "Protein_mg.cm.2" "Sym.density_10.6cells.cm.2" "Chl.a_ug.cm2" "CaCO3.Density_g.mL.1"
[11] "X.internal.volume" "pg.Chl.a.per.zoox" "AFDW_mg.cm.2" "TAC_CRE.mgprotein.1" "ug.Chl.a.per.zoox"
[16] "day" "month" "year" "season" "period" #row.has.na <- apply(mdsbefore[,(8:17)], 1, function(x){any(is.na(x))})
#mdsbefore.filtered <- mdsbefore[!row.has.na,]
#mdsbefore.filteredlibrary(vegan)
phys.rda<- rda(mdspor[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)biplot(phys.rda, scaling=1, main='Scaling')
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, mdspor)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scoresinclude_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]eig<-eigenvals(phys.rda)
eig PC1 PC2 PC3 PC4 PC5 PC6 PC7
2.8435855 1.8611869 1.2190327 0.5227434 0.3197398 0.1906720 0.0430398 gpor<-ggplot()+
geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
facet_wrap(~Coral)+
geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
scale_color_brewer(palette = "RdYlBu")+
#scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors
scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
gpor
gporseason<-ggplot()+
geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=season, shape=Bleach), size=3, alpha=0.8)+
facet_wrap(~Coral)+
geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
#scale_color_brewer(palette = "RdYlBu")+
scale_color_manual("season", values=c("summer"='indianred3', "winter"= "navyblue","NA"="white"))+
#scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors
scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
gporseason
permanova_por<-adonis(mdspor[,(7:13)] ~ Bleach*Months, data=mdspor, permutations=9999)'adonis' will be deprecated: use 'adonis2' insteadpermanova_por$aov.tab
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Bleach 1 0.0248 0.024830 0.9556 0.00622 0.4775
Months 7 0.7463 0.106610 4.1028 0.18703 0.0001 ***
Bleach:Months 7 0.1527 0.021815 0.8395 0.03827 0.7078
Residuals 118 3.0662 0.025985 0.76847
Total 133 3.9900 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$call
adonis(formula = mdspor[, (7:13)] ~ Bleach * Months, data = mdspor,
permutations = 9999)
$coefficients
Protein_mg.cm.2 Sym.density_10.6cells.cm.2 Chl.a_ug.cm2 CaCO3.Density_g.mL.1 X.internal.volume pg.Chl.a.per.zoox AFDW_mg.cm.2
(Intercept) 0.440081536 2.725992032 20.07875328 1.5517563719 38.6205787 20.4368838 8.12506185
Bleach1 -0.004401769 0.065851648 -0.45222447 0.0213482775 0.5020922 -1.0259859 -0.14242038
Months1 -0.164475063 -1.744527777 -1.34279776 -0.1094768433 -3.4307563 1.1641162 -4.26442073
Months2 -0.082818238 0.248112602 -5.97529232 -0.0051207589 2.0024258 -6.3334229 1.04936603
Months3 -0.053952488 -0.650950664 0.96263070 0.0116898580 -0.1088162 0.6045001 -3.09839846
Months4 0.083342397 0.822592216 6.72992884 0.1178511860 4.4084619 6.3717983 2.87816534
Months5 0.053571366 -0.002032736 -1.80273462 0.0613187810 1.6260016 -2.1608652 2.21010382
Months6 0.082899088 0.908619056 2.94671672 -0.0119268660 -1.8224865 2.5885862 -0.76751106
Months7 0.070425383 0.073008030 3.85388445 -0.0109457804 0.6934055 3.4957539 1.64367468
Bleach1:Months1 0.025645469 -0.032927205 1.27931564 -0.0620194244 -3.1565276 -2.7370141 0.56327481
Bleach1:Months2 0.053211317 0.538785552 1.73485695 -0.0098793343 -0.5451277 2.3086183 0.89583295
Bleach1:Months3 -0.033209169 -0.347972902 -0.87562763 0.0479799013 1.9779093 -0.3018662 -0.72337014
Bleach1:Months4 -0.068075053 0.054006786 -4.43921048 -0.0004306646 1.1879232 -3.8654491 -0.82289352
Bleach1:Months5 -0.021133363 0.010704503 0.09924784 0.0012695431 -0.1408971 0.6730092 -0.49126077
Bleach1:Months6 0.007032930 -0.247099692 0.24681577 -0.0243685792 -1.1041745 0.8205772 0.07789076
Bleach1:Months7 0.065143921 0.076166670 2.01165117 0.0481323390 0.7083978 2.5854126 1.14131808
$coef.sites
1 2 3 4 5 6 7 8 9 10 11
(Intercept) 0.143415272 0.143974600 0.1747636058 0.187562403 0.155498254 0.826012957 0.1895229600 0.216010875 0.165661019 0.171447942 0.181428177
Bleach1 -0.007270431 -0.009098197 -0.0092857099 -0.008901864 -0.011471053 0.007185291 -0.0097564286 -0.013948692 -0.012475126 -0.012387910 -0.009644987
Months1 0.032515712 0.037686145 0.0262572593 0.017257889 0.054887921 0.001411617 0.0294103442 0.027331769 0.038091786 0.047738803 0.031450102
Months2 -0.011224265 -0.023060920 -0.0355850097 -0.036535824 -0.039601767 -0.041277873 -0.0232049447 -0.048702360 -0.044088943 -0.052577463 -0.036547313
Months3 0.006589840 -0.002530762 0.0262903435 0.026746628 0.002513300 0.007022679 0.0103492863 -0.009051354 -0.007812236 0.004207399 0.019083270
Months4 0.028924330 0.025771331 0.0410611256 0.043272643 0.017252090 0.037997467 0.0435181294 0.035662185 0.025758722 0.021266136 0.039500632
Months5 -0.047955897 -0.053603191 -0.0536968612 -0.052991149 -0.056431133 0.008275896 -0.0438239832 -0.040742959 -0.049065942 -0.054022961 -0.043957819
12 13 14 15 16 17 18 19 20 21 22
(Intercept) 0.160560665 0.148906160 0.242550320 0.142385511 0.186365026 0.173839734 0.185847117 0.224895406 0.145722945 0.187094211 0.1658118849
Bleach1 -0.011742749 -0.006885517 -0.011708894 -0.006963200 -0.010727048 -0.013193845 -0.012526580 -0.004282591 -0.008664516 -0.011422749 -0.0088076047
Months1 0.057036120 0.048479110 0.046107294 0.006481671 0.031208988 0.033863395 0.035637239 0.021334305 0.011021911 -0.027402912 0.0102009630
Months2 -0.043443612 0.031968156 -0.055307839 0.006334686 -0.014488157 -0.049978533 -0.056317391 0.085696373 0.034633650 -0.012452368 0.0061974995
Months3 0.003856844 -0.005213151 0.019923202 -0.020582060 -0.030434929 -0.004220442 0.006564531 -0.033175785 -0.043968236 -0.024341614 -0.0177818234
Months4 0.015216062 -0.004797848 0.023689004 0.038309141 0.013819216 0.032707762 0.030670256 -0.016784807 0.022152949 0.067237886 0.0482275614
Months5 -0.054875470 -0.032647763 -0.046739302 -0.033954781 -0.032415478 -0.047073037 -0.052172397 0.001240707 -0.025272779 -0.024901204 -0.0295539963
23 24 25 26 27 28 29 30 31 32 33
(Intercept) 0.182463666 0.141313780 0.192339058 0.139932793 0.156178721 0.1427005334 0.228258252 0.200718402 0.200498756 0.336372531 0.161680467
Bleach1 -0.013438251 -0.008371790 -0.014183194 -0.007285381 -0.010717160 -0.0072721572 -0.006230706 -0.013776695 -0.009880892 0.002452707 -0.011421276
Months1 0.034996264 0.035062486 0.022766892 0.035353440 0.027169277 0.0119515293 -0.005776120 0.002890720 -0.007054183 0.030283774 0.016875772
Months2 -0.030042692 0.038397881 -0.032546049 0.023649816 0.014224292 0.0348532744 0.085778761 -0.037413192 0.067562510 0.087394526 0.023447186
Months3 -0.026756283 -0.034873914 -0.031154159 -0.026658859 -0.042478012 -0.0292158515 -0.049125871 -0.031920713 -0.051574584 -0.013568302 -0.049852191
Months4 0.023507915 0.005134536 0.029017226 0.015719569 0.012541531 0.0266936329 -0.002968827 0.037411268 0.022085504 -0.066564804 0.009973895
Months5 -0.037044524 -0.026915062 -0.035572364 -0.032087221 -0.028013341 -0.0241581403 0.007126289 -0.033011666 -0.004431346 0.006077281 -0.022514051
34 35 36 37 38 39 40 41 42 43 44
(Intercept) 0.154150010 0.151185896 0.153097727 0.2289204959 0.195704431 0.2234175483 0.154396911 0.147986297 0.171233422 0.145256192 0.173401715
Bleach1 -0.007431760 -0.010480724 -0.008116939 0.0004535017 -0.003602946 -0.0009426914 -0.003539756 -0.010356008 -0.003438787 -0.008363526 -0.011705069
Months1 0.022524655 0.026483962 0.005400178 0.0593920269 0.066076971 0.0470962979 0.039604953 0.052921406 0.052942451 0.066019198 0.063715555
Months2 0.053164587 0.037253911 0.028646660 0.0601558563 0.049175821 0.0778204480 0.057015962 -0.005170942 0.060516327 0.029426393 -0.044217762
Months3 -0.038452697 -0.044066865 -0.041591455 0.0008973794 -0.004369298 0.0045899924 -0.003257318 -0.018264564 -0.008849597 -0.010000091 0.005385315
Months4 -0.010253013 0.003266244 0.025965091 -0.0863531736 -0.074471026 -0.0659239829 -0.030600408 0.005136652 -0.054361591 -0.026389028 0.006174442
Months5 -0.017612364 -0.024544005 -0.027352815 -0.0154659076 -0.015261087 -0.0099547588 -0.023719325 -0.041706598 -0.016680624 -0.038712969 -0.054198375
45 46 47 48 49 50 51 52 53 54 55
(Intercept) 0.388528079 0.279783727 0.163740129 0.249570543 0.1397520100 1.758175e-01 0.167420983 0.2050325982 0.155821852 0.1937002514 0.144161816
Bleach1 -0.012991123 0.003781656 -0.006884324 0.003176204 -0.0074575915 -2.955900e-03 -0.003092993 -0.0018497524 -0.006785054 -0.0002356124 -0.004657518
Months1 0.005687773 0.041849276 0.050074843 0.046884695 0.0339847207 6.370532e-02 0.052241207 0.0655508962 0.068240387 0.0437145456 0.045417420
Months2 -0.044267359 0.067912751 0.046879484 0.070100752 -0.0100766934 5.534527e-02 0.060260759 0.0553859444 0.039876731 0.0723506139 0.053971539
Months3 -0.008873688 0.007032882 -0.002833501 0.008101709 -0.0005939787 -3.025766e-07 0.002905119 0.0008605968 -0.007280404 0.0044514120 -0.012970216
Months4 0.010858859 -0.083219936 -0.018188707 -0.083803267 0.0270336327 -5.850886e-02 -0.041225167 -0.0821976658 -0.045187098 -0.0607757450 -0.023538732
Months5 -0.024426502 -0.009760395 -0.026071886 -0.011203760 -0.0472452630 -2.577927e-02 -0.024026870 -0.0174721741 -0.033206811 -0.0103797189 -0.026274548
56 57 58 59 60 61 62 63 64 65
(Intercept) 1.518644e-01 0.1351243122 0.1653520622 0.171180439 0.1937270064 0.153436631 0.142547938 0.1948234662 0.1481496972 0.195367370
Bleach1 -8.733952e-03 -0.0064868772 -0.0054471348 -0.011546745 -0.0090300449 -0.009466828 -0.008658012 -0.0015758310 -0.0083014178 -0.007641661
Months1 2.986443e-02 0.0407210775 0.0454126807 0.035624528 0.0246553744 0.063369757 0.047665287 0.0479785505 0.0365419156 0.040547856
Months2 -2.561919e-02 0.0241907709 0.0586929222 -0.043422466 -0.0443719828 -0.013152384 -0.019153650 0.0742673576 -0.0264378547 0.047354194
Months3 1.260039e-02 -0.0076366335 -0.0051271707 0.010547879 0.0193945997 -0.003528120 -0.001522136 0.0060834668 0.0092734801 -0.018667834
Months4 3.606563e-02 0.0122761294 -0.0207288632 0.037288446 0.0421417081 -0.005257049 0.017616629 -0.0598364702 0.0326663975 0.004634243
Months5 -5.284860e-02 -0.0387421569 -0.0266158000 -0.055742543 -0.0559849207 -0.050513435 -0.053502242 -0.0128795037 -0.0539130327 -0.030291521
66 67 68 69 70 71 72 73 74 75 76
(Intercept) 0.1897240421 0.1522646904 0.1454052288 0.180343411 0.133496007 0.171413518 0.140330691 0.148645717 0.146124564 0.158685264 0.138742216
Bleach1 -0.0080432145 -0.0120424554 -0.0059897115 -0.013082041 -0.007297994 -0.013125364 -0.007680872 -0.006488933 -0.006665453 -0.004885224 -0.008336842
Months1 0.0211964697 0.0397221582 0.0489417363 0.025321341 0.045786089 0.034465069 0.058875606 0.025162912 0.031775047 0.037396093 0.033644617
Months2 -0.0365567374 -0.0314311623 0.0378497668 -0.045007985 0.012354321 -0.039027489 0.028351136 0.061115204 0.055295677 0.064683349 0.037434243
Months3 0.0277449931 -0.0085405545 -0.0038435267 -0.002044979 -0.014326270 -0.018453125 -0.011822561 -0.025416297 -0.030792296 -0.009203112 -0.035117248
Months4 0.0358734221 0.0269940374 -0.0105200567 0.042135260 0.010772469 0.029873025 -0.016563215 -0.002584284 -0.008157834 -0.020695650 0.007840745
Months5 -0.0574948569 -0.0504657152 -0.0401211507 -0.048756815 -0.044827189 -0.044084479 -0.043933543 -0.014198732 -0.018933443 -0.016740283 -0.028784256
77 78 79 80 81 82 83 84 85 86 87
(Intercept) 0.134115472 0.1423513812 0.1364923757 0.340126446 0.158171212 0.1922717706 0.1634429593 0.156028655 0.147945899 0.187376053 0.1595581926
Bleach1 -0.006950772 -0.0102025389 -0.0071303324 -0.001785590 -0.002562047 -0.0088504753 -0.0120401659 -0.007914539 -0.005768758 -0.004752466 -0.0022176414
Months1 0.037999257 0.0386515769 0.0254052960 0.046970570 0.051062961 0.0138073264 0.0334753423 0.019675502 0.049399388 0.058702557 0.0473076292
Months2 0.036330921 0.0223719300 0.0322888528 0.088897707 0.059471674 0.0497186590 -0.0387836712 0.023708879 0.051890065 0.052808581 0.0633381628
Months3 -0.018637763 -0.0356800546 -0.0233590733 -0.014534093 -0.001300150 -0.0419052813 -0.0005013061 -0.018145095 -0.018008370 -0.011960217 0.0004774617
Months4 0.006382668 0.0085109425 0.0231957362 -0.045295530 -0.039838577 0.0318596521 0.0380678877 0.035560011 -0.023875798 -0.061443351 -0.0412146346
Months5 -0.031405488 -0.0321896359 -0.0291151657 0.006271681 -0.019323033 -0.0151292936 -0.0497837511 -0.028749589 -0.022828599 -0.010777395 -0.0189363365
88 89 90 91 92 93 94 95 96 97 98
(Intercept) 0.141661530 0.1604645126 0.145296863 0.137427273 0.136090002 0.181807696 0.880911396 0.214520529 0.170654609 0.212294349 0.151586615
Bleach1 -0.005712283 -0.0031085865 -0.007310948 -0.007266042 -0.007385246 -0.003037728 0.009435480 0.001159121 -0.003234707 -0.003196141 -0.005284365
Months1 0.051086269 0.0439635153 0.029135622 0.058796109 0.031727770 0.056988906 -0.002853709 0.047594790 0.063810194 0.047418918 0.054708485
Months2 0.046671629 0.0607833293 -0.006882116 0.029904192 0.002697875 0.056487175 -0.026819846 0.071073322 0.055833219 0.074606229 0.052364721
Months3 -0.014508043 0.0006143244 0.004760298 -0.011553381 -0.014942043 -0.001140631 0.009462487 0.006442503 -0.000387974 -0.002795959 -0.013730911
Months4 -0.021972227 -0.0370908071 0.028771802 -0.014420678 0.025755239 -0.066036572 0.029929498 -0.071198461 -0.061944958 -0.044572589 -0.036829322
Months5 -0.030913877 -0.0227866515 -0.045945761 -0.041679096 -0.042048274 -0.023066931 0.011633149 -0.007882153 -0.023666950 -0.012138510 -0.023463665
99 100 101 102 103 104 105 106 107 108 109
(Intercept) 1.474973e-01 0.174227251 0.218332979 0.200361901 0.215598602 0.1429487897 0.177750741 0.1763385077 0.202539472 0.1383092767 0.158301655
Bleach1 -1.021457e-02 -0.004728805 -0.012939638 -0.002883405 -0.007453595 -0.0068697038 -0.009111817 -0.0088405178 -0.010306687 -0.0070672504 -0.006951178
Months1 4.297179e-02 0.064158604 0.042670592 0.065068705 0.014780557 0.0351658775 0.022160545 0.0324756748 0.018791016 0.0344886594 0.042922358
Months2 2.790125e-02 0.047305008 -0.055018339 0.049808593 -0.041447748 0.0056482063 -0.034085590 -0.0350902279 -0.030207549 0.0171452955 0.053943437
Months3 -2.937108e-02 -0.006234560 0.008368004 -0.004341471 0.033688081 0.0001977113 0.020148717 0.0300578195 0.015960690 -0.0064868555 -0.010292018
Months4 -8.410555e-03 -0.058669324 0.027269267 -0.075813343 0.042854585 0.0232621137 0.046770610 0.0370572954 0.054634081 0.0210241949 -0.007925930
Months5 -2.912285e-02 -0.021005678 -0.049549880 -0.015863060 -0.051863845 -0.0385404555 -0.047972104 -0.0553922843 -0.044927580 -0.0364274966 -0.022180171
110 111 112 113 114 115 116 117 118 119 120
(Intercept) 0.2676370032 0.190199220 1.587500e-01 0.159460006 0.191275606 0.190916652 0.192752127 0.2054067404 0.3652511438 0.2434098598 0.233599391
Bleach1 -0.0105757794 -0.012416199 -7.967830e-03 -0.009742940 -0.014296806 -0.004770733 -0.008289545 -0.0090393785 0.0013860657 -0.0003108801 -0.010443487
Months1 -0.0132600805 -0.014970876 2.548737e-02 0.019865217 0.017207166 0.027982876 -0.017612735 0.0046825788 -0.0046867311 0.0081457172 -0.040439650
Months2 -0.0283552915 -0.017327956 4.306342e-02 -0.019831674 -0.044382289 0.061914359 0.003466190 -0.0386409891 0.0645715067 0.0809559646 0.010753817
Months3 0.0102630804 -0.011948447 -2.779748e-02 0.003973393 -0.011390866 -0.031120610 -0.023595812 0.0155100876 -0.0236046646 -0.0158148257 -0.041728653
Months4 0.0661820931 0.069410621 2.358672e-02 0.050019735 0.043570031 -0.044852761 0.048397463 0.0532715293 -0.0475316090 -0.0465487877 0.066678396
Months5 -0.0283940604 -0.028828329 -2.045225e-02 -0.041882581 -0.042254987 -0.005770272 -0.025717108 -0.0457631968 0.0031185808 0.0064127036 -0.015586649
121 122 123 124 125 126 127 128 129 130 131
(Intercept) 0.157334564 0.244900419 0.1788629893 0.187852247 0.217134817 0.186363257 0.220490798 0.168176787 0.168347477 0.178808485 0.367644154
Bleach1 -0.009282680 -0.001495811 -0.0102661936 -0.009134805 -0.009884736 -0.010349124 -0.007866526 -0.009285452 -0.009356338 -0.003922402 -0.008604222
Months1 -0.003509105 0.016616001 -0.0192795847 -0.031176664 -0.026808949 -0.016231590 -0.017145151 -0.013473525 0.007484051 -0.003693568 -0.032402089
Months2 0.011321853 0.023218331 0.0212308375 -0.002075031 0.051716498 -0.019104641 0.062901212 -0.007750241 0.016269766 0.076781048 0.037916282
Months3 -0.040491595 0.004204989 -0.0260626263 -0.021639861 -0.050567910 -0.023039415 -0.039464755 -0.019694734 -0.018698690 -0.032726062 -0.046200075
Months4 0.032214126 -0.009124236 0.0388100388 0.057645668 0.037959585 0.051327496 0.010254830 0.053076402 0.041044726 -0.017920440 0.046915607
Months5 -0.028522929 -0.021020309 -0.0205526207 -0.025018975 -0.005464834 -0.035486873 0.001020385 -0.032141032 -0.028085150 0.001460095 -0.001716087
132 133 134
(Intercept) 0.194771422 0.267799395 0.230837067
Bleach1 -0.010848423 -0.009320292 -0.010524550
Months1 -0.033369161 -0.024715651 -0.041307081
Months2 -0.018694138 -0.008879206 -0.021497303
Months3 -0.015918964 -0.012704357 -0.005636867
Months4 0.069585944 0.051738987 0.073161441
Months5 -0.025830171 -0.025813886 -0.024825794
[ reached getOption("max.print") -- omitted 9 rows ]
$f.perms
[,1] [,2] [,3]
[1,] 0.8203163313 1.2224424 0.5166757
[2,] 1.0047472156 1.1054645 1.0152269
[3,] 1.1924792366 0.7464770 1.2389838
[4,] 0.5277109886 1.8424612 2.0265697
[5,] 0.5168676548 0.8863873 1.1574783
[6,] 0.2109609178 1.0632915 0.8734477
[7,] 0.8786852078 1.0037024 0.6193805
[8,] 0.7699045638 0.8770819 1.0561936
[9,] 1.1904820022 0.8081282 1.0683790
[10,] 0.0165912027 0.9020802 1.0215138
[11,] 0.6862364445 1.4487745 0.9643295
[12,] 1.7125850792 0.5625855 1.2154580
[13,] 0.8531635371 1.1136423 1.2154797
[14,] 1.0961516316 1.2901848 1.0276303
[15,] 0.7284360061 1.0306264 0.9226654
[16,] 0.6802437622 1.4655930 0.8542111
[17,] -0.0085740960 0.9850171 0.4497395
[18,] 1.3441793194 0.9321463 1.2901553
[19,] -0.0744321067 0.5090913 0.9627853
[20,] 0.1986603966 1.3053949 0.8570691
[21,] 0.9557695099 1.1857564 0.6495181
[22,] 2.4048508532 1.4358968 1.0676954
[23,] 1.2687271974 0.8761167 0.8809741
[24,] 1.3947636929 0.6381210 0.7018975
[25,] 0.7404791834 1.0859691 0.9272242
[26,] 0.0413543715 0.8908782 1.1451123
[27,] 0.2488460963 0.6769399 0.7818084
[28,] 1.5078686052 1.0388839 0.8269814
[29,] 1.2195907340 1.2953508 0.9081362
[30,] 0.6130710017 0.6672758 1.0146088
[31,] 0.6069297442 1.4730364 0.8923881
[32,] 0.3911038136 0.8196672 0.5136711
[33,] 0.2140514023 1.1760828 0.8657177
[34,] 0.3424095282 0.9448484 0.7614054
[35,] 0.6107659475 1.1025941 0.9969672
[36,] 0.7953021122 0.6492127 1.1967550
[37,] 1.4611631478 1.0318362 0.9277964
[38,] 0.8784486462 0.7801355 0.5600080
[39,] 0.1464128032 0.6482112 1.4935743
[40,] 1.5738387796 0.7871666 0.4282966
[41,] 0.9926492066 0.9949298 0.9731018
[42,] 0.2467377215 1.0749880 0.7041948
[43,] 1.4457318872 1.4458524 1.4291671
[44,] 1.0101297103 0.6736573 0.6978617
[45,] 1.3944825970 1.0587670 1.5950262
[46,] 0.4621516255 0.7535506 0.8961950
[47,] 0.5975043966 0.5675834 1.1199912
[48,] 2.0761345085 1.0290908 0.7775621
[49,] 1.4860945902 1.1736236 0.5673696
[50,] 0.5285156018 0.9266098 1.3558576
[51,] 0.0932682547 1.5119033 1.2771371
[52,] 2.5738056718 0.7346091 0.7925224
[53,] 1.1960355335 0.5169702 0.8165894
[54,] 0.4340133382 0.8925604 0.7859671
[55,] 0.6239261659 0.7318085 0.7528844
[56,] 1.8764254498 1.0596750 1.2760423
[57,] 1.3932072942 0.6517108 0.9535499
[58,] 0.1494986053 1.5657554 0.2573448
[59,] 0.5684206097 1.1857771 0.9418992
[60,] 1.0285029825 0.8341479 0.6243876
[61,] 1.2718408342 0.7573198 0.5126670
[62,] 0.5402530062 1.0534247 0.7289926
[63,] 0.3251465015 0.8306262 1.2122819
[64,] 1.4233904699 1.0607746 1.1169800
[65,] 1.2862274978 0.7268388 1.0879219
[66,] 0.2032577614 1.0606645 1.3823888
[67,] 0.1468379436 0.6664223 0.9365588
[68,] 0.2353490191 0.6754211 0.9381749
[69,] 1.0085186560 0.9663404 0.9831211
[70,] 0.1899066969 0.7927742 0.8937054
[71,] 1.1387579308 0.8427491 0.9855615
[72,] 0.3708505945 1.2785459 1.0041292
[73,] 1.7142074233 0.8299159 0.9554501
[74,] 1.9078733726 1.5316125 0.8366541
[75,] 1.6431651401 1.3290505 1.2689135
[76,] 0.5051666438 0.9854784 1.0353711
[77,] 2.1449016410 0.8271158 0.5866363
[78,] 1.3967013939 0.9500727 1.0647924
[79,] 0.7494397670 0.7316256 0.6768399
[80,] 0.3762742363 1.0281874 1.0949400
[81,] 1.6878276373 0.6049076 1.0162634
[82,] 1.1617396539 1.1376321 0.7314102
[83,] 1.4150142805 0.7611277 1.0997304
[84,] 0.4658207913 0.8228843 1.0262517
[85,] 0.9203390691 1.2002719 1.0579500
[86,] -0.1690849650 1.4247742 0.4321966
[87,] 0.3542281561 1.0436396 0.8800033
[88,] 4.7376727155 0.7415697 0.8941556
[89,] 0.3712811941 0.9140998 0.9058066
[90,] 0.4789472057 0.9351598 1.0579333
[91,] 0.8599330549 1.2627233 0.8973003
[92,] 0.6630169736 1.2926199 0.9333613
[93,] 1.5799367413 0.6134359 1.0299217
[94,] 0.8619897379 0.7141072 1.5828470
[95,] 2.0547061397 0.9055819 1.0315764
[96,] 1.7487257530 1.1780725 0.5468067
[97,] 1.8294236521 0.8221799 1.1590970
[98,] 0.4201063280 1.2046299 1.1166981
[99,] 0.0234860269 1.0001012 1.5163873
[100,] 0.4113478933 0.5512401 0.8671914
[101,] 0.3631969048 1.2967224 1.4971730
[102,] 0.8024345197 0.8820250 1.3212967
[103,] 0.6097755705 0.6984301 1.5446629
[104,] 1.1319112197 1.1428095 1.5705660
[105,] 1.0409147238 1.9752726 1.2555126
[106,] 0.0526593890 0.6623981 1.0859595
[107,] 0.8429134980 0.9840321 1.3223455
[108,] 0.1861250880 0.9962205 0.9610069
[109,] 1.0063484880 0.9499511 0.9326142
[110,] 0.7932906766 1.2286495 1.0545464
[111,] 1.2697293296 1.1203773 1.0544195
[112,] 1.0119303041 0.8497714 0.7380076
[113,] 1.1374888555 0.7978150 0.7403414
[114,] 0.8299038220 0.9878547 1.2806570
[115,] 0.0278511181 0.8579761 0.6993527
[116,] 0.2382402953 0.8198327 0.9288783
[117,] 0.3489933453 1.0200397 0.8656601
[118,] 1.1115224059 1.0040319 0.8243840
[119,] 1.5558586469 1.2909255 0.9578751
[120,] 0.4437572088 0.9813377 1.1150569
[121,] 0.8161264271 0.7858486 0.9655720
[122,] 0.8066605155 0.7660489 0.4709843
[123,] 0.1585657060 0.9975701 1.2093066
[124,] 0.1965563592 1.0109160 1.3838314
[125,] 0.1566165565 1.2998724 1.3412970
[126,] 0.1559691920 1.2911451 1.0878555
[127,] 0.6219887062 0.7335132 0.9934277
[128,] 0.4562746330 1.5504194 1.4483171
[129,] 0.8186048731 0.7196530 1.3861033
[130,] 2.2105640107 0.6732745 0.9382440
[131,] 0.8699606504 1.3943302 0.5742061
[132,] 0.4062519458 1.1898839 1.2362839
[133,] 2.0938465193 1.6909106 1.2622559
[134,] 0.3347050307 1.0217435 0.9420839
[135,] 2.4119313616 1.3900584 1.6298553
[136,] 0.1766389815 1.0131942 0.9372995
[137,] 0.4287274764 0.9300953 0.9828048
[138,] 0.7687941307 1.0516430 0.8217758
[139,] 1.1392047568 1.4378470 1.2728493
[140,] 0.1742521925 1.4276143 1.1213596
[141,] 0.3524410872 1.3843100 1.0678590
[142,] 1.3571571775 0.9756722 0.7881998
[143,] 1.5076902242 0.7274646 0.7106316
[144,] 0.7291005239 1.3238750 0.7045650
[145,] 1.6737873323 1.0299510 0.7842022
[146,] 1.4788730793 1.2528956 1.1883006
[147,] 2.9959057287 0.6551025 1.1929856
[148,] 3.0167784343 1.1160889 1.0446067
[149,] 0.0475831676 1.0104551 0.8214700
[150,] 2.3421149873 0.9511079 1.3057270
[151,] 1.2651892321 0.9362979 0.9412558
[152,] 0.2588207139 0.9135478 0.9171062
[153,] 0.8772507749 1.0023970 0.8565593
[154,] 0.2523333818 0.9153225 1.0017761
[155,] 0.7923933424 0.7816035 1.0902256
[156,] 0.8093646013 1.1895848 0.8529394
[157,] 0.0173017194 0.7944248 0.6790745
[158,] 1.2995406821 0.6998135 1.0298570
[159,] 2.6756371079 0.7467849 0.6757335
[160,] 1.3210855544 1.0417339 1.0443175
[161,] 0.8583777293 0.7534789 0.8131577
[162,] 0.7689971254 0.9008098 0.6954497
[163,] 0.1933781773 1.2465135 1.2588498
[164,] 0.8137926010 0.5592021 0.6740301
[165,] 2.2706258838 0.9497357 1.2870687
[166,] 1.0887784181 1.0993572 0.7604207
[167,] 0.5101072661 1.0132813 1.2327701
[168,] 1.3522305752 1.0171758 0.8828411
[169,] 0.6228431504 0.9786157 1.0156819
[170,] 0.9171784422 0.5862561 0.7846244
[171,] 0.3581102293 1.9890537 1.4140756
[172,] 1.2342676711 0.9059722 1.1101091
[173,] 2.3368403980 1.0032489 0.7945030
[174,] 0.2163495915 1.0021542 1.5152251
[175,] 0.5719187896 0.7626133 0.4076421
[176,] 1.3237350940 1.3991432 1.0014613
[177,] 0.9643471286 1.1750816 0.5498475
[178,] 0.2468207757 0.4622806 0.9861318
[179,] 1.0834942864 0.6957781 0.6779190
[180,] 1.7093570242 1.0825238 1.1143300
[181,] 1.5228132028 0.8359382 0.6900032
[182,] 0.8790493081 0.9831376 0.9629848
[183,] 2.4352582110 1.3058436 0.7079138
[184,] 0.7768855459 1.2571089 0.7263910
[185,] 0.2438184150 1.5024157 0.9270089
[186,] 1.2022139885 1.5285478 1.0395958
[187,] 0.3163209626 0.7600630 0.9116461
[188,] 0.6363497473 0.8552696 1.4086663
[189,] -0.0940691842 0.9613853 0.6830546
[190,] 0.8261986353 1.4287992 0.6310124
[191,] 0.8286453657 0.5958106 0.6052458
[192,] 1.4391676307 0.6300058 1.1451281
[193,] 0.0832406691 0.7745085 0.9677553
[194,] 1.3534753328 1.0497275 1.0944980
[195,] 1.4610936380 0.6060614 0.9538243
[196,] 2.7736037038 0.7263079 0.7613543
[197,] 0.9266932652 0.6621170 1.0116955
[198,] 0.6782001573 1.1982817 1.3405878
[199,] 0.7278452755 1.1072897 1.5503432
[200,] 1.4057976785 1.0661749 1.1061077
[201,] 2.4419508566 0.9978945 1.0896496
[202,] 1.7246030971 0.8664659 0.8844677
[203,] 1.3992932528 1.8385933 1.4047857
[204,] 0.9086398609 0.9928240 1.4351789
[205,] 0.3521951501 0.6760973 1.0226634
[206,] 2.3599488419 0.9377734 0.7000950
[207,] 0.4157822574 0.9154733 1.0275365
[208,] 0.9116270056 0.8488302 1.0057992
[209,] 1.0667478181 0.9412318 0.8056974
[210,] -0.0258659201 1.1364995 0.9922408
[211,] 1.5007403635 0.9422955 0.7922278
[212,] 0.7397537006 1.0304036 1.0556614
[213,] 0.5939247559 0.6812818 0.8511529
[214,] 0.7332379696 0.7113773 1.0314888
[215,] 0.8948296341 0.7994133 0.8580527
[216,] 0.1931412949 0.8785835 0.9661729
[217,] 0.9954281332 1.4848782 0.9308404
[218,] 1.9290707932 1.1780531 1.0645611
[219,] 0.8689899322 1.2013303 0.4418495
[220,] 1.3320721237 0.8822500 1.0658621
[221,] 0.3909052016 0.8448367 0.7669075
[222,] 1.6010299858 0.8060332 1.2922285
[223,] 0.1867497007 0.8529514 1.0770596
[224,] 2.4873885086 1.3575382 1.4668288
[225,] 1.0920338306 0.8571329 1.2052192
[226,] 1.0338397669 1.2986796 1.0608942
[227,] 1.2384847600 0.8985667 0.9399026
[228,] 1.0941709812 0.8826582 1.0305047
[229,] 1.1232899578 0.8988907 0.5574315
[230,] 0.9905074185 1.1265256 1.2351581
[231,] 1.1834352317 0.8225555 0.8866787
[232,] 0.3471883061 0.7762697 1.3530211
[233,] 0.4154948419 0.9732803 0.7185646
[234,] 1.3126383057 1.0322439 1.1080824
[235,] 0.5048669596 0.6024866 0.9913120
[236,] 0.5541699718 0.9535838 0.7801490
[237,] 1.4737939880 1.0382573 1.1201448
[238,] 0.2589905146 1.0167347 0.7976945
[239,] 0.1465818137 1.5457320 0.5517120
[240,] 1.1598441413 0.6869919 0.7888790
[241,] 0.4701744653 0.8784352 0.9336546
[242,] 0.8794211888 0.7840671 0.7267768
[243,] 3.3196622893 0.6954792 0.9515357
[244,] 1.5981104256 1.1696895 1.6534356
[245,] 0.7948935757 0.6720091 0.9461148
[246,] 3.4021210225 1.4463869 0.7454375
[247,] 1.1634834378 0.7057810 0.9562009
[248,] 0.8234564112 0.9358819 0.9147473
[249,] 3.1233225809 1.0494257 1.0109184
[250,] 0.5801488423 1.3957541 0.7770132
[251,] 1.4542582418 0.9174745 1.0613594
[252,] 0.9506971187 1.1898015 0.9765897
[253,] 1.3647380696 0.7591765 1.0001409
[254,] 2.2174881638 0.8208483 1.1070598
[255,] 0.4695012609 1.3032361 1.0962814
[256,] 1.0960058455 1.0575517 0.7085621
[257,] 1.6422476182 1.2533772 0.7824459
[258,] 0.3600209359 0.8069392 1.0932405
[259,] 0.2430000439 1.1207837 1.5838102
[260,] 1.2697662728 1.1983350 1.1434338
[261,] 0.5301943128 1.0936972 0.8852202
[262,] 0.4698318155 1.0981273 0.7776010
[263,] 1.8609800730 0.9570613 0.9631925
[264,] 1.3772116330 1.1826249 1.1948397
[265,] 0.3828203906 1.5513556 1.7565027
[266,] 1.4243184019 0.9049825 0.8325656
[267,] 1.0707193015 0.8683536 0.9425915
[268,] 0.7373173593 0.9768423 1.1389128
[269,] 0.1330659494 1.2884559 1.0604327
[270,] 1.1869535484 0.7942008 0.9205236
[271,] 0.0802777642 1.0895198 1.2193309
[272,] 1.0508403254 1.0189060 0.5544736
[273,] 1.5677809927 1.4665497 0.9291901
[274,] 0.6410307922 0.9119278 1.1188765
[275,] 1.9768016346 0.9639034 0.6574226
[276,] 3.4538558734 1.6941004 1.4281572
[277,] 0.4326027086 0.7953091 1.3121507
[278,] 0.2348820632 0.7176688 1.0099313
[279,] 1.5217336198 1.7844457 0.8877096
[280,] 0.1349753286 0.4749218 0.8502372
[281,] 1.0008725151 0.7455790 0.7749107
[282,] 0.7148759597 0.8409594 0.8176921
[283,] 0.4795914874 0.9449842 0.9870568
[284,] 0.3123816933 0.9731055 1.1545142
[285,] 0.6008516081 1.4034447 0.5481770
[286,] 0.7554468264 1.5995914 1.3457539
[287,] 0.5353969993 0.8336640 0.6348469
[288,] 0.1155734517 0.7968340 0.7394196
[289,] 0.1937235128 1.1482186 0.7221255
[290,] 1.6230257938 0.9793055 2.2130926
[291,] 0.8650927300 0.9303359 0.9346058
[292,] 0.7113932277 1.0678338 0.7042027
[293,] 1.2033660156 0.8297856 0.9582085
[294,] -0.0027969324 1.0262609 0.8681980
[295,] 0.0641554415 1.0658990 0.7570812
[296,] 1.9996043924 0.5260666 0.9542580
[297,] 0.8458598314 1.2325118 0.9225543
[298,] 0.8771435709 0.9793808 0.6152738
[299,] 1.8330409312 1.0103735 1.1275606
[300,] 0.5160567413 1.3123603 0.9584948
[301,] 0.9643460530 0.6834833 1.0212811
[302,] 1.9051361417 0.7202998 0.8208726
[303,] 0.8002450708 1.1160332 0.9548409
[304,] 2.8526296407 1.0106770 0.7697626
[305,] 0.7926077019 1.2384339 0.2235800
[306,] 2.4808297628 1.0702016 0.7865719
[307,] 1.6898722819 0.7763566 1.0780317
[308,] 0.1206456612 0.7210747 1.1088523
[309,] 0.3750418936 0.7718568 0.6722961
[310,] 0.6214237955 1.3500443 1.5080532
[311,] 0.0291849775 1.2038191 1.2632615
[312,] 1.1758321792 0.9341728 0.6520794
[313,] 0.4154951384 1.0622831 1.2668280
[314,] 0.3781346580 1.0755100 1.2497409
[315,] 0.3378931913 1.0072737 0.3369583
[316,] 1.3310330326 0.9679176 0.9070138
[317,] 0.3370777769 1.1011325 1.0777736
[318,] 0.3207075973 1.3381196 0.9098232
[319,] 0.1398897309 1.2084749 0.9670409
[320,] 1.6389382661 1.0894651 0.7630211
[321,] 1.0097503507 1.0052987 1.3641059
[322,] 0.3529854425 1.3036231 0.7575702
[323,] 0.3731991853 0.6984965 1.1113991
[324,] 0.6480608416 0.9933208 1.0907704
[325,] 0.4151018004 0.9786664 1.4513501
[326,] 0.1615499706 0.9519803 0.9030657
[327,] 0.3656604686 0.7957820 1.0073540
[328,] 0.6676169050 0.9687906 0.8721180
[329,] 0.4894650454 0.7471410 1.3316736
[330,] 0.6948517165 1.2471345 0.8112373
[331,] 0.1610315136 0.8659728 1.0739100
[332,] 0.0029123565 0.8206561 0.7703789
[333,] -0.1232232282 1.0923935 1.5091217
[ reached getOption("max.print") -- omitted 9666 rows ]
$model.matrix
(Intercept) Bleach1 Months1 Months2 Months3 Months4 Months5 Months6 Months7 Bleach1:Months1 Bleach1:Months2 Bleach1:Months3 Bleach1:Months4 Bleach1:Months5
1 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
2 1 1 0 1 0 0 0 0 0 0 1 0 0 0
3 1 1 0 1 0 0 0 0 0 0 1 0 0 0
4 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
5 1 1 0 1 0 0 0 0 0 0 1 0 0 0
6 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
7 1 1 0 1 0 0 0 0 0 0 1 0 0 0
8 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
9 1 1 0 1 0 0 0 0 0 0 1 0 0 0
10 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
11 1 1 0 1 0 0 0 0 0 0 1 0 0 0
12 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
13 1 1 0 1 0 0 0 0 0 0 1 0 0 0
14 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
15 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
16 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
17 1 1 0 1 0 0 0 0 0 0 1 0 0 0
18 1 -1 0 1 0 0 0 0 0 0 -1 0 0 0
19 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
20 1 1 0 0 1 0 0 0 0 0 0 1 0 0
21 1 1 0 0 1 0 0 0 0 0 0 1 0 0
22 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
23 1 1 0 0 1 0 0 0 0 0 0 1 0 0
24 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
25 1 1 0 0 1 0 0 0 0 0 0 1 0 0
26 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
27 1 1 0 0 1 0 0 0 0 0 0 1 0 0
28 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
29 1 1 0 0 1 0 0 0 0 0 0 1 0 0
30 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
31 1 1 0 0 1 0 0 0 0 0 0 1 0 0
32 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
33 1 1 0 0 1 0 0 0 0 0 0 1 0 0
34 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
35 1 1 0 0 1 0 0 0 0 0 0 1 0 0
36 1 -1 0 0 1 0 0 0 0 0 0 -1 0 0
37 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
38 1 1 0 0 0 1 0 0 0 0 0 0 1 0
39 1 1 0 0 0 1 0 0 0 0 0 0 1 0
40 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
41 1 1 0 0 0 1 0 0 0 0 0 0 1 0
42 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
43 1 1 0 0 0 1 0 0 0 0 0 0 1 0
44 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
45 1 1 0 0 0 1 0 0 0 0 0 0 1 0
46 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
47 1 1 0 0 0 1 0 0 0 0 0 0 1 0
48 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
49 1 1 0 0 0 1 0 0 0 0 0 0 1 0
50 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
51 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
52 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
53 1 1 0 0 0 1 0 0 0 0 0 0 1 0
54 1 -1 0 0 0 1 0 0 0 0 0 0 -1 0
55 1 -1 0 0 0 0 1 0 0 0 0 0 0 -1
56 1 1 0 0 0 0 1 0 0 0 0 0 0 1
57 1 1 0 0 0 0 1 0 0 0 0 0 0 1
58 1 -1 0 0 0 0 1 0 0 0 0 0 0 -1
59 1 1 0 0 0 0 1 0 0 0 0 0 0 1
60 1 -1 0 0 0 0 1 0 0 0 0 0 0 -1
61 1 1 0 0 0 0 1 0 0 0 0 0 0 1
62 1 -1 0 0 0 0 1 0 0 0 0 0 0 -1
Bleach1:Months6 Bleach1:Months7
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 0 0
14 0 0
15 0 0
16 0 0
17 0 0
18 0 0
19 0 0
20 0 0
21 0 0
22 0 0
23 0 0
24 0 0
25 0 0
26 0 0
27 0 0
28 0 0
29 0 0
30 0 0
31 0 0
32 0 0
33 0 0
34 0 0
35 0 0
36 0 0
37 0 0
38 0 0
39 0 0
40 0 0
41 0 0
42 0 0
43 0 0
44 0 0
45 0 0
46 0 0
47 0 0
48 0 0
49 0 0
50 0 0
51 0 0
52 0 0
53 0 0
54 0 0
55 0 0
56 0 0
57 0 0
58 0 0
59 0 0
60 0 0
61 0 0
62 0 0
[ reached getOption("max.print") -- omitted 72 rows ]
$terms
mdspor[, (7:13)] ~ Bleach * Months
attr(,"variables")
list(mdspor[, (7:13)], Bleach, Months)
attr(,"factors")
Bleach Months Bleach:Months
mdspor[, (7:13)] 0 0 0
Bleach 1 0 1
Months 0 1 1
attr(,"term.labels")
[1] "Bleach" "Months" "Bleach:Months"
attr(,"order")
[1] 1 1 2
attr(,"intercept")
[1] 1
attr(,"response")
[1] 1
attr(,".Environment")
<environment: R_GlobalEnv>
attr(,"class")
[1] "adonis"library(pairwiseAdonis)
pairwise.adonis2(mdspor[,(7:13)] ~Months, data=mdspor, permutations = 9999, na.rm=T)'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead
'adonis' will be deprecated: use 'adonis2' instead$parent_call
[1] "mdspor[, (7:13)] ~ Months , strata = Null"
$`10_vs_13`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.15927 0.159273 5.178 0.13217 1e-04 ***
Residuals 34 1.04582 0.030759 0.86783
Total 35 1.20509 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`10_vs_17`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.23959 0.239588 7.4378 0.17949 1e-04 ***
Residuals 34 1.09522 0.032212 0.82051
Total 35 1.33481 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`10_vs_20`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.05841 0.058407 2.1402 0.05922 0.0191 *
Residuals 34 0.92785 0.027290 0.94078
Total 35 0.98626 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`10_vs_24`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.18750 0.187497 6.211 0.17152 1e-04 ***
Residuals 30 0.90563 0.030188 0.82848
Total 31 1.09313 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`10_vs_29`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.14954 0.149541 2.8868 0.08275 0.0095 **
Residuals 32 1.65768 0.051803 0.91725
Total 33 1.80722 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`10_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.03927 0.039273 1.2559 0.04293 0.2626
Residuals 28 0.87559 0.031271 0.95707
Total 29 0.91486 1.00000
$`10_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.1621 0.16210 4.4435 0.10987 1e-04 ***
Residuals 36 1.3133 0.03648 0.89013
Total 37 1.4754 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`13_vs_17`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.10838 0.108380 6.003 0.15006 0.0072 **
Residuals 34 0.61384 0.018054 0.84994
Total 35 0.72222 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`13_vs_20`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.06488 0.064880 4.9408 0.12688 0.0143 *
Residuals 34 0.44648 0.013132 0.87312
Total 35 0.51136 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`13_vs_24`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.02787 0.027871 1.9708 0.06164 0.1572
Residuals 30 0.42425 0.014142 0.93836
Total 31 0.45212 1.00000
$`13_vs_29`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.06926 0.069264 1.8842 0.05561 0.0536 .
Residuals 32 1.17631 0.036760 0.94439
Total 33 1.24557 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`13_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.11916 0.119156 8.4633 0.2321 5e-04 ***
Residuals 28 0.39421 0.014079 0.7679
Total 29 0.51337 1.0000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`13_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.03183 0.031827 1.3773 0.03685 0.2467
Residuals 36 0.83189 0.023108 0.96315
Total 37 0.86371 1.00000
$`17_vs_20`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.09198 0.091982 6.3068 0.15647 0.0057 **
Residuals 34 0.49587 0.014585 0.84353
Total 35 0.58786 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`17_vs_24`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.05867 0.058666 3.7157 0.11021 0.0319 *
Residuals 30 0.47365 0.015788 0.88979
Total 31 0.53232 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`17_vs_29`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.03095 0.030950 0.80803 0.02463 0.6089
Residuals 32 1.22570 0.038303 0.97537
Total 33 1.25665 1.00000
$`17_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.21502 0.215018 13.572 0.32646 2e-04 ***
Residuals 28 0.44361 0.015843 0.67354
Total 29 0.65863 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`17_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.23063 0.23063 9.4212 0.20742 1e-04 ***
Residuals 36 0.88128 0.02448 0.79258
Total 37 1.11192 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`20_vs_24`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.06691 0.066914 6.5541 0.1793 0.0049 **
Residuals 30 0.30629 0.010210 0.8207
Total 31 0.37320 1.0000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`20_vs_29`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.06759 0.067588 2.0436 0.06003 0.0265 *
Residuals 32 1.05834 0.033073 0.93997
Total 33 1.12592 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`20_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.04354 0.043538 4.413 0.13615 0.0156 *
Residuals 28 0.27625 0.009866 0.86385
Total 29 0.31978 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`20_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.10132 0.101322 5.1093 0.12429 5e-04 ***
Residuals 36 0.71392 0.019831 0.87571
Total 37 0.81524 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`24_vs_29`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.04044 0.040437 1.0928 0.03756 0.3432
Residuals 28 1.03611 0.037004 0.96244
Total 29 1.07655 1.00000
$`24_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.12941 0.129408 12.226 0.3375 3e-04 ***
Residuals 24 0.25402 0.010584 0.6625
Total 25 0.38343 1.0000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`24_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.09915 0.099154 4.5872 0.12538 0.0043 **
Residuals 32 0.69170 0.021615 0.87462
Total 33 0.79085 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`29_vs_35`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.15556 0.155562 4.0202 0.13392 0.0011 **
Residuals 26 1.00608 0.038695 0.86608
Total 27 1.16164 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`29_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.14544 0.145443 3.4252 0.09152 0.0031 **
Residuals 34 1.44375 0.042463 0.90848
Total 35 1.58919 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$`35_vs_0`
Permutation: free
Number of permutations: 9999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Months 1 0.08846 0.088464 4.011 0.11793 0.0052 **
Residuals 30 0.66166 0.022055 0.88207
Total 31 0.75012 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
attr(,"class")
[1] "pwadstrata" "list" library(cowplot)
pcaillustrator<-cowplot::plot_grid(gmon,gpor,g, nrow=3,ncol=2, align="h", axis = "bt")
pcaillustrator
#STHS ##Temperature data
amb<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/AMB_21257937.csv")
mild<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/3C_21257935.csv")
mod<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/6C_21257936.csv")
ex<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/9C_20473299.csv")
amb<- plyr::rename(amb, c("ï..Date"="Date"))
amb$Date<-as.Date(amb$Date)
amb$Treatment<-as.factor(amb$Treatment)
ambmild<- plyr::rename(mild, c("ï..Date"="Date"))
mild$Date<-as.Date(mild$Date)
mild$Treatment<-as.factor(mild$Treatment)
mildmod<- plyr::rename(mod, c("ï..Date"="Date"))
mod$Date<-as.Date(mod$Date)
mod$Treatment<-as.factor(mod$Treatment)
modex<- plyr::rename(ex, c("ï..Date"="Date"))
ex$Date<-as.Date(ex$Date)
ex$Treatment<-as.factor(ex$Treatment)
exalltemp<- merge(amb, mild, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp<- merge(alltemp, mod, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp<- merge(alltemp, ex, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp$Date_Time<- as.POSIXct(paste(alltemp$Date, alltemp$Time), "%Y-%m-%d hh:mm:ss")Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'alltemp$Treatment<-as.factor(alltemp$Treatment)
alltemp$hour <- as.POSIXlt(alltemp$Date_Time)$hourWarning: unknown timezone '%Y-%m-%d hh:mm:ss'alltempWarning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone '%Y-%m-%d hh:mm:ss'unique(alltemp$hour) [1] 19 20 21 22 23 0 1 10 11 12 13 14 15 16 17 18 2 3 4 5 6 7 8 9#write.csv(alltemp, "Short-term heat stress temperature data.csv")tempsub<-filter(alltemp, Date == c("2022-09-01", "2022-09-02","2022-09-03"))Warning: longer object length is not a multiple of shorter object lengthWarning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone '%Y-%m-%d hh:mm:ss'tempsubWarning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone '%Y-%m-%d hh:mm:ss'tempsub_mean<-summarySE(tempsub, measurevar='Temperature', na.rm=TRUE, conf.interval = 0.95)
tempsub_meanalltemp_mean<-summarySE(alltemp, measurevar='Temperature', groupvars=c('Treatment', "Date", "hour"), na.rm=TRUE, conf.interval = 0.95)Warning: NaNs producedalltemp_meansths.lm<- lm(Temperature~Treatment, data=alltemp_mean) #Gaussian
car::Anova(sths.lm)Anova Table (Type II tests)
Response: Temperature
Sum Sq Df F value Pr(>F)
Treatment 13.07 3 3.0398 0.02907 *
Residuals 510.28 356
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(sths.lm, list(pairwise ~ Treatment), adjust = "tukey")
tukey3$`emmeans of Treatment`
Treatment emmean SE df lower.CL upper.CL
AMB 28.1 0.126 356 27.9 28.4
3C 28.4 0.126 356 28.1 28.6
6C 28.6 0.126 356 28.3 28.8
9C 28.6 0.126 356 28.4 28.9
Confidence level used: 0.95
$`pairwise differences of Treatment`
1 estimate SE df t.ratio p.value
AMB - 3C -0.2392 0.178 356 -1.340 0.5380
AMB - 6C -0.4133 0.178 356 -2.316 0.0963
AMB - 9C -0.4982 0.178 356 -2.792 0.0282
3C - 6C -0.1742 0.178 356 -0.976 0.7633
3C - 9C -0.2591 0.178 356 -1.452 0.4681
6C - 9C -0.0849 0.178 356 -0.476 0.9644
P value adjustment: tukey method for comparing a family of 4 estimates par(mfrow=c(2,3))
plot(sths.lm, ask=FALSE, which=1:6)
lims <- as.POSIXct(strptime(c("2022-09-04 00:00", "2022-09-05 0:00"),
format = "%Y-%m-%d %H:%M"))
alltemp$Date<- as.Date(as.POSIXct(alltemp$Date, origin="1970-01-01"))
STHS_hobo_temp<-ggplot(alltemp, aes(y=Temperature, x=Date_Time, color=Treatment))+
geom_line(size=1)+
#geom_hline(yintercept = 27.7, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
geom_hline(yintercept = 28.7, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
scale_x_datetime(labels = date_format("%H:%M"), breaks = date_breaks("3 hours"),limits=lims, expand=c(0.015,0.015))+
scale_y_continuous(expression(Temperature~(degree~C)))+
scale_color_brewer(palette ="RdBu", direction =-1)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(),
legend.position=c(0.89,0.80),
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger
STHS_hobo_temptempfigs<-cowplot::plot_grid(STHS_hobo_temp, STHS_hobo_temp,STHS_hobo_temp, STHS_hobo_temp, nrow = 2, ncol = 2)Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).tempfigs
##PAM
pam<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/PAM data for STHS.csv")
pam$Treatment<- as.factor(pam$Treatment)
pam$Bleach<-as.factor(pam$Bleach)
#pam$Months<-as.factor(pam$Months)
pam$Species<-as.factor(pam$Species)
pam$Colony.ID<-as.factor(pam$Colony.ID)
pam$Rep<-as.factor(pam$Rep)
pam$Temperature<- as.numeric(pam$Temperature)
pamlibrary(Rmisc)
allpamsum<-summarySE(pam, measurevar='Y', groupvars=c('Treatment',"Temperature",'Species','Bleach',"Colony.ID"), na.rm=TRUE, conf.interval = 0.95)
allpamsum###Normality
hist(allpamsum$Y)
sths.lm<- lm(Y~Treatment*Species*Bleach, data=allpamsum) #Gaussian
par(mfrow=c(2,3))
plot(sths.lm, ask=FALSE, which=1:6)
###Stats
Y.lme <- lme(Y~Treatment*Species*Bleach, random = ~1|Colony.ID, data=allpamsum, na.action=na.exclude)
car::Anova(Y.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Y
Chisq Df Pr(>Chisq)
(Intercept) 1030.2318 1 < 2.2e-16 ***
Treatment 348.3408 3 < 2.2e-16 ***
Species 2.8518 1 0.09127 .
Bleach 0.1034 1 0.74779
Treatment:Species 35.3168 3 1.044e-07 ***
Treatment:Bleach 9.1089 3 0.02788 *
Species:Bleach 0.2096 1 0.64706
Treatment:Species:Bleach 4.4031 3 0.22110
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(Y.lme, list(pairwise ~ Treatment:Species), adjust = "tukey", simple="Species")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Treatment, Species`
Treatment Species emmean SE df lower.CL upper.CL
3C Montipora capitata 0.687 0.0152 36 0.656 0.718
6C Montipora capitata 0.667 0.0152 36 0.636 0.698
9C Montipora capitata 0.281 0.0152 36 0.250 0.312
AMB Montipora capitata 0.709 0.0152 36 0.678 0.740
3C Porites compressa 0.645 0.0152 36 0.614 0.676
6C Porites compressa 0.628 0.0152 36 0.597 0.659
9C Porites compressa 0.398 0.0152 36 0.367 0.428
AMB Porites compressa 0.672 0.0152 36 0.641 0.703
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Treatment, Species | Treatment`
Treatment = 3C:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.0416 0.0216 36 1.930 0.0615
Treatment = 6C:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.0390 0.0216 36 1.810 0.0787
Treatment = 9C:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa -0.1163 0.0216 36 -5.394 <.0001
Treatment = AMB:
2 estimate SE df t.ratio p.value
Montipora capitata - Porites compressa 0.0375 0.0216 36 1.741 0.0902
Results are averaged over the levels of: Bleach
Degrees-of-freedom method: containment tukey2<- emmeans(Y.lme, list(pairwise ~ Treatment:Bleach), adjust = "tukey", simple="Bleach")NOTE: Results may be misleading due to involvement in interactionstukey2$`emmeans of Treatment, Bleach`
Treatment Bleach emmean SE df lower.CL upper.CL
3C Bleach 0.666 0.0152 36 0.635 0.697
6C Bleach 0.646 0.0152 36 0.615 0.677
9C Bleach 0.311 0.0152 36 0.280 0.342
AMB Bleach 0.687 0.0152 36 0.656 0.718
3C Non-bleach 0.666 0.0152 36 0.635 0.697
6C Non-bleach 0.649 0.0152 36 0.618 0.680
9C Non-bleach 0.368 0.0152 36 0.337 0.399
AMB Non-bleach 0.694 0.0152 36 0.663 0.725
Results are averaged over the levels of: Species
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Treatment, Bleach | Treatment`
Treatment = 3C:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -6.67e-05 0.0216 36 -0.003 0.9975
Treatment = 6C:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -2.77e-03 0.0216 36 -0.128 0.8986
Treatment = 9C:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -5.68e-02 0.0216 36 -2.638 0.0122
Treatment = AMB:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -7.15e-03 0.0216 36 -0.332 0.7420
Results are averaged over the levels of: Species
Degrees-of-freedom method: containment summary(Y.lme)Linear mixed-effects model fit by REML
Data: allpamsum
Random effects:
Formula: ~1 | Colony.ID
(Intercept) Residual
StdDev: 0.009235533 0.06751884
Fixed effects: Y ~ Treatment * Species * Bleach Correlation:
(Intr) Trtm6C Trtm9C TrtAMB SpcsPc BlchN- Tr6C:SPc Tr9C:SPc TrAMB:SPc T6C:BN T9C:BN
Treatment6C -0.701
Treatment9C -0.701 0.500
TreatmentAMB -0.701 0.500 0.500
SpeciesPorites compressa -0.707 0.495 0.495 0.495
BleachNon-bleach -0.707 0.495 0.495 0.495 0.500
Treatment6C:SpeciesPorites compressa 0.495 -0.707 -0.354 -0.354 -0.701 -0.350
Treatment9C:SpeciesPorites compressa 0.495 -0.354 -0.707 -0.354 -0.701 -0.350 0.500
TreatmentAMB:SpeciesPorites compressa 0.495 -0.354 -0.354 -0.707 -0.701 -0.350 0.500 0.500
Treatment6C:BleachNon-bleach 0.495 -0.707 -0.354 -0.354 -0.350 -0.701 0.500 0.250 0.250
Treatment9C:BleachNon-bleach 0.495 -0.354 -0.707 -0.354 -0.350 -0.701 0.250 0.500 0.250 0.500
TreatmentAMB:BleachNon-bleach 0.495 -0.354 -0.354 -0.707 -0.350 -0.701 0.250 0.250 0.500 0.500 0.500
SpeciesPorites compressa:BleachNon-bleach 0.500 -0.350 -0.350 -0.350 -0.707 -0.707 0.495 0.495 0.495 0.495 0.495
Treatment6C:SpeciesPorites compressa:BleachNon-bleach -0.350 0.500 0.250 0.250 0.495 0.495 -0.707 -0.354 -0.354 -0.707 -0.354
Treatment9C:SpeciesPorites compressa:BleachNon-bleach -0.350 0.250 0.500 0.250 0.495 0.495 -0.354 -0.707 -0.354 -0.354 -0.707
TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach -0.350 0.250 0.250 0.500 0.495 0.495 -0.354 -0.354 -0.707 -0.354 -0.354
TAMB:B SPc:BN T6C:SPc: T9C:SPc:
Treatment6C
Treatment9C
TreatmentAMB
SpeciesPorites compressa
BleachNon-bleach
Treatment6C:SpeciesPorites compressa
Treatment9C:SpeciesPorites compressa
TreatmentAMB:SpeciesPorites compressa
Treatment6C:BleachNon-bleach
Treatment9C:BleachNon-bleach
TreatmentAMB:BleachNon-bleach
SpeciesPorites compressa:BleachNon-bleach 0.495
Treatment6C:SpeciesPorites compressa:BleachNon-bleach -0.354 -0.701
Treatment9C:SpeciesPorites compressa:BleachNon-bleach -0.354 -0.701 0.500
TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach -0.707 -0.701 0.500 0.500
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-4.308757602 -0.237332187 -0.008017678 0.235385651 4.251163970
Number of Observations: 160
Number of Groups: 40 r.squaredGLMM(Y.lme) R2m R2c
[1,] 0.8261913 0.8293836####Coefficients
coef(Y.lme) (Intercept) Treatment6C Treatment9C TreatmentAMB SpeciesPorites compressa BleachNon-bleach Treatment6C:SpeciesPorites compressa
3 0.6885504 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
4 0.6930096 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
11 0.6963025 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
12 0.6910078 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
19 0.6916605 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
20 0.6891394 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
26 0.6914929 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
27 0.6917337 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
41 0.6887918 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
42 0.6938370 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
43 0.6872890 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
44 0.6905355 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
45 0.6908111 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
46 0.6891719 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
201 0.6892932 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
202 0.6915184 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
203 0.6887245 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
204 0.6915300 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
209 0.6899604 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
210 0.6923075 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
211 0.6950898 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
212 0.6926731 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
213 0.6888870 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
214 0.6897835 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
219 0.6948461 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
220 0.6918839 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
221 0.6936856 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
222 0.6941469 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
225 0.6973330 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
226 0.6902743 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
235 0.6908691 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
236 0.6935237 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
237 0.6882986 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
238 0.6911621 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
239 0.6940082 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
240 0.6906225 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
243 0.6935092 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
244 0.6932162 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
247 0.6943563 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
248 0.6931639 -0.0239 -0.4604 0.0191 -0.05146667 -0.0098 0.007633333
Treatment9C:SpeciesPorites compressa TreatmentAMB:SpeciesPorites compressa Treatment6C:BleachNon-bleach Treatment9C:BleachNon-bleach
3 0.2108333 0.003533333 0.007733333 0.1097667
4 0.2108333 0.003533333 0.007733333 0.1097667
11 0.2108333 0.003533333 0.007733333 0.1097667
12 0.2108333 0.003533333 0.007733333 0.1097667
19 0.2108333 0.003533333 0.007733333 0.1097667
20 0.2108333 0.003533333 0.007733333 0.1097667
26 0.2108333 0.003533333 0.007733333 0.1097667
27 0.2108333 0.003533333 0.007733333 0.1097667
41 0.2108333 0.003533333 0.007733333 0.1097667
42 0.2108333 0.003533333 0.007733333 0.1097667
43 0.2108333 0.003533333 0.007733333 0.1097667
44 0.2108333 0.003533333 0.007733333 0.1097667
45 0.2108333 0.003533333 0.007733333 0.1097667
46 0.2108333 0.003533333 0.007733333 0.1097667
201 0.2108333 0.003533333 0.007733333 0.1097667
202 0.2108333 0.003533333 0.007733333 0.1097667
203 0.2108333 0.003533333 0.007733333 0.1097667
204 0.2108333 0.003533333 0.007733333 0.1097667
209 0.2108333 0.003533333 0.007733333 0.1097667
210 0.2108333 0.003533333 0.007733333 0.1097667
211 0.2108333 0.003533333 0.007733333 0.1097667
212 0.2108333 0.003533333 0.007733333 0.1097667
213 0.2108333 0.003533333 0.007733333 0.1097667
214 0.2108333 0.003533333 0.007733333 0.1097667
219 0.2108333 0.003533333 0.007733333 0.1097667
220 0.2108333 0.003533333 0.007733333 0.1097667
221 0.2108333 0.003533333 0.007733333 0.1097667
222 0.2108333 0.003533333 0.007733333 0.1097667
225 0.2108333 0.003533333 0.007733333 0.1097667
226 0.2108333 0.003533333 0.007733333 0.1097667
235 0.2108333 0.003533333 0.007733333 0.1097667
236 0.2108333 0.003533333 0.007733333 0.1097667
237 0.2108333 0.003533333 0.007733333 0.1097667
238 0.2108333 0.003533333 0.007733333 0.1097667
239 0.2108333 0.003533333 0.007733333 0.1097667
240 0.2108333 0.003533333 0.007733333 0.1097667
243 0.2108333 0.003533333 0.007733333 0.1097667
244 0.2108333 0.003533333 0.007733333 0.1097667
247 0.2108333 0.003533333 0.007733333 0.1097667
248 0.2108333 0.003533333 0.007733333 0.1097667
TreatmentAMB:BleachNon-bleach SpeciesPorites compressa:BleachNon-bleach Treatment6C:SpeciesPorites compressa:BleachNon-bleach
3 0.006533333 0.01973333 -0.01006667
4 0.006533333 0.01973333 -0.01006667
11 0.006533333 0.01973333 -0.01006667
12 0.006533333 0.01973333 -0.01006667
19 0.006533333 0.01973333 -0.01006667
20 0.006533333 0.01973333 -0.01006667
26 0.006533333 0.01973333 -0.01006667
27 0.006533333 0.01973333 -0.01006667
41 0.006533333 0.01973333 -0.01006667
42 0.006533333 0.01973333 -0.01006667
43 0.006533333 0.01973333 -0.01006667
44 0.006533333 0.01973333 -0.01006667
45 0.006533333 0.01973333 -0.01006667
46 0.006533333 0.01973333 -0.01006667
201 0.006533333 0.01973333 -0.01006667
202 0.006533333 0.01973333 -0.01006667
203 0.006533333 0.01973333 -0.01006667
204 0.006533333 0.01973333 -0.01006667
209 0.006533333 0.01973333 -0.01006667
210 0.006533333 0.01973333 -0.01006667
211 0.006533333 0.01973333 -0.01006667
212 0.006533333 0.01973333 -0.01006667
213 0.006533333 0.01973333 -0.01006667
214 0.006533333 0.01973333 -0.01006667
219 0.006533333 0.01973333 -0.01006667
220 0.006533333 0.01973333 -0.01006667
221 0.006533333 0.01973333 -0.01006667
222 0.006533333 0.01973333 -0.01006667
225 0.006533333 0.01973333 -0.01006667
226 0.006533333 0.01973333 -0.01006667
235 0.006533333 0.01973333 -0.01006667
236 0.006533333 0.01973333 -0.01006667
237 0.006533333 0.01973333 -0.01006667
238 0.006533333 0.01973333 -0.01006667
239 0.006533333 0.01973333 -0.01006667
240 0.006533333 0.01973333 -0.01006667
243 0.006533333 0.01973333 -0.01006667
244 0.006533333 0.01973333 -0.01006667
247 0.006533333 0.01973333 -0.01006667
248 0.006533333 0.01973333 -0.01006667
Treatment9C:SpeciesPorites compressa:BleachNon-bleach TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach
3 -0.1059667 0.0011
4 -0.1059667 0.0011
11 -0.1059667 0.0011
12 -0.1059667 0.0011
19 -0.1059667 0.0011
20 -0.1059667 0.0011
26 -0.1059667 0.0011
27 -0.1059667 0.0011
41 -0.1059667 0.0011
42 -0.1059667 0.0011
43 -0.1059667 0.0011
44 -0.1059667 0.0011
45 -0.1059667 0.0011
46 -0.1059667 0.0011
201 -0.1059667 0.0011
202 -0.1059667 0.0011
203 -0.1059667 0.0011
204 -0.1059667 0.0011
209 -0.1059667 0.0011
210 -0.1059667 0.0011
211 -0.1059667 0.0011
212 -0.1059667 0.0011
213 -0.1059667 0.0011
214 -0.1059667 0.0011
219 -0.1059667 0.0011
220 -0.1059667 0.0011
221 -0.1059667 0.0011
222 -0.1059667 0.0011
225 -0.1059667 0.0011
226 -0.1059667 0.0011
235 -0.1059667 0.0011
236 -0.1059667 0.0011
237 -0.1059667 0.0011
238 -0.1059667 0.0011
239 -0.1059667 0.0011
240 -0.1059667 0.0011
243 -0.1059667 0.0011
244 -0.1059667 0.0011
247 -0.1059667 0.0011
248 -0.1059667 0.0011allpamsum2<-summarySE(pam, measurevar='Y', groupvars=c('Treatment',"Temperature",'Species','Bleach'), na.rm=TRUE, conf.interval = 0.95)
allpamsum2###Figure
allpamsum$Treatment <- factor(allpamsum$Treatment, levels=c("AMB","3C","6C","9C"))
allpamsum$Temperature<- factor(allpamsum$Temperature, levels =c("27.7","30.7","33.7","36.7"))
allpamsum$Bleach<- factor(allpamsum$Bleach, levels =c("Non-bleach","Bleach"))
allpamsum2$Treatment <- factor(allpamsum2$Treatment, levels=c("AMB","3C","6C","9C"))
allpamsum2$Temperature<- factor(allpamsum2$Temperature, levels =c("27.7","30.7","33.7","36.7"))
allpamsum2$Bleach<- factor(allpamsum2$Bleach, levels =c("Non-bleach","Bleach"))
pamfig<-ggplot(allpamsum2, aes(y=Y, x=Treatment, color=Bleach))+
geom_point(data=allpamsum, aes(y=Y,x=Treatment, color=Bleach),alpha=0.5,position=position_jitterdodge(0.05))+
geom_path(aes(stat="identity"), position=position_dodge(0.5))+
facet_wrap(~Species, nrow=1)+
geom_point(size=1, position=position_dodge(0.5),stat="identity")+
geom_errorbar(aes(ymin=Y-se, ymax=Y+se, width= 0.5), position=position_dodge(0.5),stat="identity") +
scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.50,0.75))+
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_blank(),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12, face="italic"))Warning: Ignoring unknown aesthetics: statpamfig
ed50m<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Montipora ed50.csv")
ed50m$Bleach<-as.factor(ed50m$Bleach)
ed50med50p<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Porites ed50.csv")
ed50p$Bleach<-as.factor(ed50p$Bleach)
ed50pallpamsumporites<-filter(allpamsum, Species == "Porites compressa")
allpamsummontipora<-filter(allpamsum, Species == "Montipora capitata")#Porites DRM model
library(drc) #if not working, ensure temperature is numeric
sths.drc.por <- drm(Y~Temperature, fct=LL.3(),
data = allpamsumporites,
curveid = Bleach)Error in optim(startVec, opfct, hessian = TRUE, method = optMethod, control = list(maxit = maxIt, :
non-finite value supplied by optim
Error in drmOpt(opfct, opdfct1, startVecSc, optMethod, constrained, warnVal, :
Convergence failedAICc(sths.drc.por, sths.drc.por2)##Create predictions data frame
newdata = with(allpamsumporites,
expand.grid(Bleach = levels(Bleach),
Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.por, newdata=newdata, interval = "confidence", level=0.95))Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>%
group_by(Bleach,Temperature) %>%
summarise_all(.funs=mean)
pred.averagepam.fig.por<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
annotate("rect",xmin=36.94588, xmax=37.41424, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
annotate("rect", xmin=37.01656, xmax=37.53534,ymin=-Inf, ymax=Inf, fill= "#796334", alpha = 0.1) +
geom_line(size=1)+
geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.4, show.legend = FALSE) +
geom_point(data=allpamsumporites, aes(y=Y, x=Temperature, color=Bleach),alpha=0.7,position=position_jitterdodge(0.05))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.5,0.75))+
geom_vline(xintercept = 37.180062, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
geom_vline(xintercept = 37.27595, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
#geom_point(data = ed50p, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
pam.fig.por
library(drc)
sths.drc.mon <- drm(Y~Temperature, fct=LL.3(),
data = allpamsummontipora,
curveid = Bleach)Warning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedsummary(sths.drc.mon)# run model.
Model fitted: Log-logistic (ED50 as parameter) with lower limit at 0 (3 parms)
Parameter estimates:
Estimate Std. Error t-value p-value
b:Bleach 43.116793 9.646432 4.4697 2.77e-05 ***
b:Non-bleach 37.135455 10.942992 3.3935 0.001111 **
d:Bleach 0.701765 0.015795 44.4303 < 2.2e-16 ***
d:Non-bleach 0.695647 0.016136 43.1116 < 2.2e-16 ***
e:Bleach 36.100733 0.175850 205.2930 < 2.2e-16 ***
e:Non-bleach 36.606397 0.135508 270.1411 < 2.2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error:
0.06902043 (74 degrees of freedom)plot(sths.drc.mon)
ed50<-ED(sths.drc.mon, 50, interval="delta")Warning: NAs introduced by coercion
Estimated effective doses
Estimate Std. Error Lower Upper
e:Bleach:50 36.10073 0.17585 35.75034 36.45112
e:Non-bleach:50 36.60640 0.13551 36.33639 36.87640ed50 Estimate Std. Error Lower Upper
e:Bleach:50 36.10073 0.1758498 35.75034 36.45112
e:Non-bleach:50 36.60640 0.1355084 36.33639 36.87640##Create predictions data frame
newdata = with(allpamsummontipora,
expand.grid(Bleach = levels(Bleach),
Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.mon, newdata=newdata, interval = "confidence", level=0.95))Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>%
group_by(Bleach,Temperature) %>%
summarise_all(.funs=mean)
pred.averagepam.fig.mon<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
annotate("rect",xmin=35.92488, xmax=36.27658, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
annotate("rect", xmin=36.47089, xmax=36.74191,ymin=-Inf, ymax=Inf, fill= "#796334", alpha = 0.1) +
geom_line(size=1)+
geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.4, show.legend = FALSE) +
geom_point(data=allpamsummontipora, aes(y=Y, x=Temperature, color=Bleach),alpha=0.7,position=position_jitterdodge(0.05))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.5,0.75))+
geom_vline(xintercept = 36.100733, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
geom_vline(xintercept = 36.606397, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
#geom_point(data = ed50m, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.2),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
pam.fig.mon
pamfig2<-ggplot(allpamsum, aes(y=Y, x=Temperature, color=Bleach, fill=Bleach))+
geom_point(alpha=0.5)+
geom_smooth(method=drm, method.args=list(fct=L.3()), se=F)+
facet_grid(~Species)+
#scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+
#scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.8), breaks=c(0,0.25,0.50,0.75))+
#geom_hline(yintercept=0.4)+
geom_vline(xintercept =c(36.23238), linetype='solid', size=1, color='#DFD3B9')+
geom_vline(xintercept =c(37.08728), linetype='dashed', size=1, color='#DFD3B9')+
geom_vline(xintercept =c(36.622434), linetype='solid', size=1, color='#796334')+
geom_vline(xintercept =c(37.185249), linetype='dashed', size=1, color='#796334')+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.12,0.15),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(size=12, face="italic"))
pamfig2
pamfigs<-cowplot::plot_grid(pamfig2, pamfig2, nrow = 2, ncol = 1)`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'pamfigs
##Color score
color<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Color score data STHS.csv")
color$Treatment<- as.factor(color$Treatment)
color$Bleach<-as.factor(color$Bleach)
#color$Months<-as.factor(color$Months)
color$Species<-as.factor(color$Species)
color$Colony.ID<-as.factor(color$Colony.ID)
#color$Rep<-as.factor(color$Rep)
color###Normality
hist(color$Color_avg)
sthsc.lm<- lm(Color_avg~Treatment*Species*Bleach, data=color) #Gaussian
par(mfrow=c(2,3))
plot(sthsc.lm, ask=FALSE, which=1:6)
###Stats
color.lme <- lme(Color_avg~Treatment*Species*Bleach, random = ~1|Colony.ID, data=color, na.action=na.exclude)
car::Anova(color.lme, type=3)Warning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedWarning: one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omittedAnalysis of Deviance Table (Type III tests)
Response: Color_avg
Chisq Df Pr(>Chisq)
(Intercept) 195.0162 1 < 2.2e-16 ***
Treatment 134.0736 3 < 2.2e-16 ***
Species 7.4448 1 0.006362 **
Bleach 6.7526 1 0.009361 **
Treatment:Species 5.4485 3 0.141749
Treatment:Bleach 3.5958 3 0.308551
Species:Bleach 4.0853 1 0.043257 *
Treatment:Species:Bleach 1.0530 3 0.788433
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1tukey3<- emmeans(color.lme, list(pairwise ~ Species:Bleach), adjust = "tukey", simple="Bleach")NOTE: Results may be misleading due to involvement in interactionstukey3$`emmeans of Species, Bleach`
Species Bleach emmean SE df lower.CL upper.CL
Montipora capitata Bleach 0.535 0.0272 39 0.480 0.590
Porites compressa Bleach 0.703 0.0272 37 0.647 0.758
Montipora capitata Non-bleach 0.690 0.0272 39 0.635 0.745
Porites compressa Non-bleach 0.695 0.0272 37 0.640 0.750
Results are averaged over the levels of: Treatment
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Species, Bleach | Species`
Species = Montipora capitata:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) -0.1550 0.0385 107 -4.028 0.0001
Species = Porites compressa:
2 estimate SE df t.ratio p.value
Bleach - (Non-bleach) 0.0075 0.0385 37 0.195 0.8465
Results are averaged over the levels of: Treatment
Degrees-of-freedom method: containment tukey2<- emmeans(color.lme, list(pairwise ~ Treatment), adjust = "tukey")NOTE: Results may be misleading due to involvement in interactionstukey2$`emmeans of Treatment`
Treatment emmean SE df lower.CL upper.CL
3 0.9100 0.0272 37 0.8549 0.9651
6 0.7300 0.0272 37 0.6749 0.7851
9 0.0275 0.0272 37 -0.0276 0.0826
AMB 0.9550 0.0272 37 0.8999 1.0101
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
Confidence level used: 0.95
$`pairwise differences of Treatment`
1 estimate SE df t.ratio p.value
3 - 6 0.180 0.0385 107 4.677 <.0001
3 - 9 0.882 0.0385 107 22.933 <.0001
3 - AMB -0.045 0.0385 107 -1.169 0.6474
6 - 9 0.703 0.0385 107 18.255 <.0001
6 - AMB -0.225 0.0385 107 -5.847 <.0001
9 - AMB -0.927 0.0385 107 -24.102 <.0001
Results are averaged over the levels of: Species, Bleach
Degrees-of-freedom method: containment
P value adjustment: tukey method for comparing a family of 4 estimates summary(color.lme)Linear mixed-effects model fit by REML
Data: color
Random effects:
Formula: ~1 | Colony.ID
(Intercept) Residual
StdDev: 8.038071e-06 0.172099
Fixed effects: Color_avg ~ Treatment * Species * Bleach Correlation:
(Intr) Trtmn6 Trtmn9 TrtAMB SpcsPc BlchN- Tr6:SPc Tr9:SPc TrAMB:SPc T6:BN- T9:BN-
Treatment6 -0.707
Treatment9 -0.707 0.500
TreatmentAMB -0.707 0.500 0.500
SpeciesPorites compressa -0.707 0.500 0.500 0.500
BleachNon-bleach -0.707 0.500 0.500 0.500 0.500
Treatment6:SpeciesPorites compressa 0.500 -0.707 -0.354 -0.354 -0.707 -0.354
Treatment9:SpeciesPorites compressa 0.500 -0.354 -0.707 -0.354 -0.707 -0.354 0.500
TreatmentAMB:SpeciesPorites compressa 0.500 -0.354 -0.354 -0.707 -0.707 -0.354 0.500 0.500
Treatment6:BleachNon-bleach 0.500 -0.707 -0.354 -0.354 -0.354 -0.707 0.500 0.250 0.250
Treatment9:BleachNon-bleach 0.500 -0.354 -0.707 -0.354 -0.354 -0.707 0.250 0.500 0.250 0.500
TreatmentAMB:BleachNon-bleach 0.500 -0.354 -0.354 -0.707 -0.354 -0.707 0.250 0.250 0.500 0.500 0.500
SpeciesPorites compressa:BleachNon-bleach 0.500 -0.354 -0.354 -0.354 -0.707 -0.707 0.500 0.500 0.500 0.500 0.500
Treatment6:SpeciesPorites compressa:BleachNon-bleach -0.354 0.500 0.250 0.250 0.500 0.500 -0.707 -0.354 -0.354 -0.707 -0.354
Treatment9:SpeciesPorites compressa:BleachNon-bleach -0.354 0.250 0.500 0.250 0.500 0.500 -0.354 -0.707 -0.354 -0.354 -0.707
TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach -0.354 0.250 0.250 0.500 0.500 0.500 -0.354 -0.354 -0.707 -0.354 -0.354
TAMB:B SPc:BN T6:SPc: T9:SPc:
Treatment6
Treatment9
TreatmentAMB
SpeciesPorites compressa
BleachNon-bleach
Treatment6:SpeciesPorites compressa
Treatment9:SpeciesPorites compressa
TreatmentAMB:SpeciesPorites compressa
Treatment6:BleachNon-bleach
Treatment9:BleachNon-bleach
TreatmentAMB:BleachNon-bleach
SpeciesPorites compressa:BleachNon-bleach 0.500
Treatment6:SpeciesPorites compressa:BleachNon-bleach -0.354 -0.707
Treatment9:SpeciesPorites compressa:BleachNon-bleach -0.354 -0.707 0.500
TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach -0.707 -0.707 0.500 0.500
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-4.357958e+00 -2.324244e-01 1.267565e-10 2.905305e-01 2.672881e+00
Number of Observations: 160
Number of Groups: 40 r.squaredGLMM(color.lme) R2m R2c
[1,] 0.8315664 0.8315664####Coefficients
coef(color.lme) (Intercept) Treatment6 Treatment9 TreatmentAMB SpeciesPorites compressa BleachNon-bleach Treatment6:SpeciesPorites compressa
3 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
4 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
11 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
12 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
19 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
20 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
26 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
27 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
41 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
42 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
43 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
44 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
45 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
46 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
201 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
202 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
203 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
204 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
209 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
210 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
211 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
212 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
213 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
214 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
219 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
220 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
221 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
222 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
225 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
226 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
235 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
236 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
237 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
238 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
239 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
240 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
243 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
244 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
247 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
248 0.76 -0.22 -0.74 0.06 0.21 0.2 0.05
Treatment9:SpeciesPorites compressa TreatmentAMB:SpeciesPorites compressa Treatment6:BleachNon-bleach Treatment9:BleachNon-bleach
3 -0.19 -0.03 0.01 -0.17
4 -0.19 -0.03 0.01 -0.17
11 -0.19 -0.03 0.01 -0.17
12 -0.19 -0.03 0.01 -0.17
19 -0.19 -0.03 0.01 -0.17
20 -0.19 -0.03 0.01 -0.17
26 -0.19 -0.03 0.01 -0.17
27 -0.19 -0.03 0.01 -0.17
41 -0.19 -0.03 0.01 -0.17
42 -0.19 -0.03 0.01 -0.17
43 -0.19 -0.03 0.01 -0.17
44 -0.19 -0.03 0.01 -0.17
45 -0.19 -0.03 0.01 -0.17
46 -0.19 -0.03 0.01 -0.17
201 -0.19 -0.03 0.01 -0.17
202 -0.19 -0.03 0.01 -0.17
203 -0.19 -0.03 0.01 -0.17
204 -0.19 -0.03 0.01 -0.17
209 -0.19 -0.03 0.01 -0.17
210 -0.19 -0.03 0.01 -0.17
211 -0.19 -0.03 0.01 -0.17
212 -0.19 -0.03 0.01 -0.17
213 -0.19 -0.03 0.01 -0.17
214 -0.19 -0.03 0.01 -0.17
219 -0.19 -0.03 0.01 -0.17
220 -0.19 -0.03 0.01 -0.17
221 -0.19 -0.03 0.01 -0.17
222 -0.19 -0.03 0.01 -0.17
225 -0.19 -0.03 0.01 -0.17
226 -0.19 -0.03 0.01 -0.17
235 -0.19 -0.03 0.01 -0.17
236 -0.19 -0.03 0.01 -0.17
237 -0.19 -0.03 0.01 -0.17
238 -0.19 -0.03 0.01 -0.17
239 -0.19 -0.03 0.01 -0.17
240 -0.19 -0.03 0.01 -0.17
243 -0.19 -0.03 0.01 -0.17
244 -0.19 -0.03 0.01 -0.17
247 -0.19 -0.03 0.01 -0.17
248 -0.19 -0.03 0.01 -0.17
TreatmentAMB:BleachNon-bleach SpeciesPorites compressa:BleachNon-bleach Treatment6:SpeciesPorites compressa:BleachNon-bleach
3 -0.02 -0.22 0.04
4 -0.02 -0.22 0.04
11 -0.02 -0.22 0.04
12 -0.02 -0.22 0.04
19 -0.02 -0.22 0.04
20 -0.02 -0.22 0.04
26 -0.02 -0.22 0.04
27 -0.02 -0.22 0.04
41 -0.02 -0.22 0.04
42 -0.02 -0.22 0.04
43 -0.02 -0.22 0.04
44 -0.02 -0.22 0.04
45 -0.02 -0.22 0.04
46 -0.02 -0.22 0.04
201 -0.02 -0.22 0.04
202 -0.02 -0.22 0.04
203 -0.02 -0.22 0.04
204 -0.02 -0.22 0.04
209 -0.02 -0.22 0.04
210 -0.02 -0.22 0.04
211 -0.02 -0.22 0.04
212 -0.02 -0.22 0.04
213 -0.02 -0.22 0.04
214 -0.02 -0.22 0.04
219 -0.02 -0.22 0.04
220 -0.02 -0.22 0.04
221 -0.02 -0.22 0.04
222 -0.02 -0.22 0.04
225 -0.02 -0.22 0.04
226 -0.02 -0.22 0.04
235 -0.02 -0.22 0.04
236 -0.02 -0.22 0.04
237 -0.02 -0.22 0.04
238 -0.02 -0.22 0.04
239 -0.02 -0.22 0.04
240 -0.02 -0.22 0.04
243 -0.02 -0.22 0.04
244 -0.02 -0.22 0.04
247 -0.02 -0.22 0.04
248 -0.02 -0.22 0.04
Treatment9:SpeciesPorites compressa:BleachNon-bleach TreatmentAMB:SpeciesPorites compressa:BleachNon-bleach
3 0.15 0.04
4 0.15 0.04
11 0.15 0.04
12 0.15 0.04
19 0.15 0.04
20 0.15 0.04
26 0.15 0.04
27 0.15 0.04
41 0.15 0.04
42 0.15 0.04
43 0.15 0.04
44 0.15 0.04
45 0.15 0.04
46 0.15 0.04
201 0.15 0.04
202 0.15 0.04
203 0.15 0.04
204 0.15 0.04
209 0.15 0.04
210 0.15 0.04
211 0.15 0.04
212 0.15 0.04
213 0.15 0.04
214 0.15 0.04
219 0.15 0.04
220 0.15 0.04
221 0.15 0.04
222 0.15 0.04
225 0.15 0.04
226 0.15 0.04
235 0.15 0.04
236 0.15 0.04
237 0.15 0.04
238 0.15 0.04
239 0.15 0.04
240 0.15 0.04
243 0.15 0.04
244 0.15 0.04
247 0.15 0.04
248 0.15 0.04allcolorsumporites<-filter(color, Species == "Porites compressa")
allcolorsumporitesallcolorsummontipora<-filter(color, Species == "Montipora capitata")
allcolorsummontipora#Porites DRM model
library(drc)
sths.drc.por <- drm(Color_avg~Temperature, fct=LL.3(),
data = allcolorsumporites,
curveid = Bleach)Warning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedsths.drc.por2 <- drm(Color_avg~Temperature, fct=L.3(),
data = allcolorsumporites,
curveid = Bleach)
summary(sths.drc.por)# run model.
Model fitted: Log-logistic (ED50 as parameter) with lower limit at 0 (3 parms)
Parameter estimates:
Estimate Std. Error t-value p-value
b:Bleach 53.968752 8.535776 6.3227 1.749e-08 ***
b:Non-bleach 87.328481 69.595102 1.2548 0.2135
d:Bleach 0.985832 0.019418 50.7696 < 2.2e-16 ***
d:Non-bleach 0.974925 0.019245 50.6582 < 2.2e-16 ***
e:Bleach 34.623068 0.167834 206.2933 < 2.2e-16 ***
e:Non-bleach 34.380959 0.550561 62.4472 < 2.2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error:
0.08602735 (74 degrees of freedom)plot(sths.drc.por)
ed50<-ED(sths.drc.por, 50, interval="delta")Warning: NAs introduced by coercion
Estimated effective doses
Estimate Std. Error Lower Upper
e:Bleach:50 34.62307 0.16783 34.28865 34.95748
e:Non-bleach:50 34.38096 0.55056 33.28394 35.47797ed50 Estimate Std. Error Lower Upper
e:Bleach:50 34.62307 0.1678342 34.28865 34.95748
e:Non-bleach:50 34.38096 0.5505607 33.28394 35.47797##Create predictions data frame
newdata = with(allcolorsumporites,
expand.grid(Bleach = levels(Bleach),
Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.por, newdata=newdata, interval = "confidence", level=0.95))Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>%
group_by(Bleach,Temperature) %>%
summarise_all(.funs=mean)
pred.averagecolor.fig.por<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
annotate("rect",xmin=33.8304, xmax=34.93152, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
annotate("rect", xmin=34.45524, xmax=34.7909, ymin=-Inf, ymax=Inf, fill= "#796334", alpha = 0.1) +
geom_line(size=1)+
geom_point(data=allcolorsumporites, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
#geom_segment(data = ed50p, aes(y=Estimate,yend=-0.1, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = 1.5)+
#geom_point(data = ed50p, aes(y=Estimate, x = ed50),size=3)+
#geom_point(size=1, position=position_dodge(0.5),stat="identity")+
#geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5), position=position_dodge(0.5),stat="identity") +
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
#scale_y_continuous(expression(Color~score),limits=c(-.25,1.1), breaks=c(-0.25,0,.25,.5,.75,1.0))+
geom_vline(xintercept = 34.62307, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
geom_vline(xintercept = 34.38096, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
#geom_point(data = ed50p, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
color.fig.por
color.fig.por2<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
geom_line(size=1)+
#geom_segment(data = ed50p, aes(y=Estimate,yend=0, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = .5)+
#geom_point(data = ed50p, aes(y=Estimate, x = ed50),size=1)+
geom_point(data=allcolorsumporites, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
#geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
#geom_point(size=1, position=position_dodge(0.5),stat="identity")+
#geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5), position=position_dodge(0.5),stat="identity") +
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
scale_y_continuous(expression(Color~score))+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position="none",
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
color.fig.por2
library(drc)
sths.drc.mon <- drm(Color_avg~Temperature, fct=LL.3(),
data = allcolorsummontipora,
curveid = Bleach)Warning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedWarning: NaNs producedsummary(sths.drc.mon)# run model.
Model fitted: Log-logistic (ED50 as parameter) with lower limit at 0 (3 parms)
Parameter estimates:
Estimate Std. Error t-value p-value
b:Bleach 49.046481 35.920317 1.3654 0.17626
b:Non-bleach 47.647123 18.087832 2.6342 0.01026 *
d:Bleach 0.792351 0.051863 15.2778 < 2e-16 ***
d:Non-bleach 0.982078 0.051365 19.1194 < 2e-16 ***
e:Bleach 34.221465 0.437561 78.2096 < 2e-16 ***
e:Non-bleach 34.537109 0.382610 90.2671 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error:
0.2253141 (74 degrees of freedom)plot(sths.drc.mon)
ed50<-ED(sths.drc.mon, 50, interval="delta")Warning: NAs introduced by coercion
Estimated effective doses
Estimate Std. Error Lower Upper
e:Bleach:50 34.22147 0.43756 33.34961 35.09332
e:Non-bleach:50 34.53711 0.38261 33.77474 35.29948ed50 Estimate Std. Error Lower Upper
e:Bleach:50 34.22147 0.4375612 33.34961 35.09332
e:Non-bleach:50 34.53711 0.3826100 33.77474 35.29948##Create predictions data frame
newdata = with(allcolorsummontipora,
expand.grid(Bleach = levels(Bleach),
Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.mon, newdata=newdata, interval = "confidence", level=0.95))Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning: Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>%
group_by(Bleach,Temperature) %>%
summarise_all(.funs=mean)
pred.averageed50m<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Montipora ed50 color.csv")
ed50m$Bleach<-as.factor(ed50m$Bleach)
ed50mcolor.fig.mon<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
#geom_segment(data = ed50m, aes(y=Estimate,yend=-.10, xend=ed50, x = ed50, color=Bleach),linetype = 1, size =1.5)+
geom_line(size=1)+
annotate("rect",xmin=33.78391, xmax=34.65903, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
annotate("rect", xmin=34.1545, xmax=34.91972, ymin=-Inf, ymax=Inf, fill= "#796334", alpha = 0.1) +
geom_point(data=allcolorsummontipora, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
#geom_point(size=1, position=position_dodge(0.5),stat="identity")+
#geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5), position=position_dodge(0.5),stat="identity") +
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
scale_y_continuous(expression(Color~score),limits=c(-.25,1.1),breaks=c(-0.25,0,.25,.5,.75,1.0))+
geom_vline(xintercept = 34.22147, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
#geom_rect(aes(xmin=33.34961, xmax=35.09332, ymin=Inf, ymax=Inf), alpha = 0.8,color = "#DFD3B9",fill = "#DFD3B9")+
geom_vline(xintercept = 34.53711, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
#geom_point(data = ed50m, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.2),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
color.fig.mon
color.fig.mon2<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
geom_line(size=1)+
#geom_segment(data = ed50m, aes(y=Estimate,yend=0, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = 2)+
#geom_point(data = ed50m, aes(y=Estimate, x = ed50),size=3)+
geom_point(data=allcolorsummontipora, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
#geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
#geom_point(size=1, position=position_dodge(0.5),stat="identity")+
#geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5), position=position_dodge(0.5),stat="identity") +
scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
scale_y_continuous(expression(Color~score))+
#scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, size=12),
axis.text.y=element_text(vjust=0.5, size=12),
axis.title.x=element_text(size=12),
axis.title.y=element_text(size=12),
legend.text = element_text(vjust=0.5, size=12),
legend.position=c(0.15,0.2),
panel.background= element_rect(fill=NA, color='black'),
strip.text = element_text(vjust=0.5, size=12))
color.fig.mon2
colorfigs<-cowplot::plot_grid(color.fig.mon, color.fig.por, nrow = 1, ncol = 2)
colorfigs
colorfigs2<-cowplot::plot_grid(color.fig.mon2, color.fig.por2, nrow = 1, ncol = 2)
colorfigs2
hobo2<-cowplot::plot_grid(STHS_hobo_temp,STHS_hobo_temp, nrow = 2, ncol = 1)Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).hobo2
pamcolorfigsall<-cowplot::plot_grid(pam.fig.mon,pam.fig.por, color.fig.mon, color.fig.por,pam.fig.mon,pam.fig.por, color.fig.mon, color.fig.por,nrow = 4, ncol = 3)
pamcolorfigsall
pamcolorfigswithtemp<-cowplot::plot_grid(STHS_hobo_temp,pamcolorfigsall,nrow = 1, ncol = 2, rel_widths = c(1,2))Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: unknown timezone '%Y-%m-%d hh:mm:ss'Warning: Removed 1044 row(s) containing missing values (geom_path).pamcolorfigswithtemp
---
title: "R Notebook"
output:
  html_notebook: default
  html_document:
    df_print: paged
  pdf_document: default
---
```{r}
library(dplyr)
library(tidyr)
library(Rmisc)
library(lubridate)
library(ggplot2)
library(car)
library(MASS)
library(mgcv)
library(MuMIn)
library(emmeans)
library(ggrepel)
library(effects)
library(lme4)
library(nlme)
library(sjPlot)
library(drc)
library(scales)
library(xfun)
```
#KBay pairs physiology
```{r}
phys<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Phys data for R with Teegan no Oct-Nov 2020 and only peak bleaching.csv", strip.white=T)
phys$Date<- as.Date(phys$Date, format = "%Y-%m-%d")
phys$Bleach<-as.factor(phys$Bleach)
phys$Months<-as.factor(phys$Months)
phys$Species<-as.factor(phys$Species)
phys$Coral_ID<-as.factor(phys$Coral_ID)
phys
```
```{r}
unique(phys$Months)
```

```{r}
phys_stress= filter(phys, Months %in% c("0","12","24","35"))
phys_stress
```

##Endolothics
```{r}
endolith<- glm(Endolithic ~ Species*Bleach*Months, data = phys, family = "binomial")
#summary(endolith)
car::Anova(endolith, type=3)
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
endofig<-ggplot(phys, aes(y=Endolithic, x=Date, color=Bleach, fill=Bleach))+ 
  geom_jitter()+
  #geom_smooth(method="loess")+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Presence~of~endolithic~algae))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        #legend.position=c(0.15,0.85),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
endofig
```

##Protein
###Normality
```{r}
hist(phys$Protein_mg.cm.2)
```

```{r}
protein.lm<- lm(Protein_mg.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(protein.lm, ask=FALSE, which=1:6)
```
```{r}
library(MuMIn)
summary(protein.lme)
r.squaredGLMM(protein.lme)
#coef(protein.lme)
```

###Stats
```{r}
protein.lme <- lme(Protein_mg.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(protein.lme, type=3)
tukey3<- emmeans(protein.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Species")
tukey3
```

```{r}
summary(protein.lme)
r.squaredGLMM(protein.lme)
```
####Coefficients
```{r}
coef(protein.lme)
```

```{r}
proteinavg<-summarySE(phys, measurevar='Protein_mg.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
proteinavg
```


###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
proteinfig<-ggplot(phys, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
proteinfig
```

```{r}
library(Rmisc)
protein_sum<-summarySE(phys, measurevar='Protein_mg.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
protein_sum
```

```{r}
proteinfig_3<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.8),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
proteinfig_3
```

```{r}
proteinfig_2<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  #geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.8),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
proteinfig_2
```


```{r}
proteinfig_3<-ggplot(protein_sum, aes(y=Protein_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=Protein_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.8),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
proteinfig_3
```


```{r}
library(Rmisc)
protein_stress<-summarySE(phys_stress, measurevar='Protein_mg.cm.2', groupvars=c('Months','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
protein_stress
```


```{r}
protein_stress_fig<-ggplot(protein_stress, aes(y=Protein_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+ 
  geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  facet_grid(~Species)+
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
protein_stress_fig
```


```{r}
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
protein_stress_fig2<-ggplot(protein_stress, aes(y=Protein_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+ 
  #geom_boxplot(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
  #geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
  geom_point(size=1.5, position= pd)+
  geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
  facet_grid(~Species)+
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3))+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Protein~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
protein_stress_fig2
```


##AFDW
###Normality
```{r}
hist(phys$AFDW_mg.cm.2)
```

```{r}
AFDW.lm<- lm(AFDW_mg.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(AFDW.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
AFDW.lme <- lme(AFDW_mg.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(AFDW.lme, type=3)
tukey3<- emmeans(AFDW.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```

```{r}
summary(AFDW.lme)
r.squaredGLMM(AFDW.lme)
```
####Coefficients
```{r}
coef(AFDW.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
AFDWfig<-ggplot(phys, aes(y=AFDW_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Total~biomass~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
AFDWfig
```

```{r}
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
AFDW_stress_fig<-ggplot(phys_stress, aes(y=AFDW_mg.cm.2, x=Months, color=Bleach, fill=Bleach))+ 
 geom_point(data=phys_stress,aes(y=AFDW_mg.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=AFDW_mg.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  #geom_point(size=1.5, position= pd)+
  #geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Total~biomass~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
AFDW_stress_fig
```

```{r}
library(Rmisc)
AFDW_sum<-summarySE(phys, measurevar='AFDW_mg.cm.2', groupvars=c('Date'), na.rm=TRUE, conf.interval = 0.95)
AFDW_sum
```

```{r}
AFDWfig_3<-ggplot(AFDW_sum, aes(y=AFDW_mg.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=AFDW_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=AFDW_mg.cm.2-se, ymax=AFDW_mg.cm.2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(AFDW~(mg~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
AFDWfig_3
```

##Lipids
###Normality
```{r}
hist(phys$Lipid..g.per.cm2.)
```

```{r}
lipid.lm<- lm(Lipid..g.per.cm2.~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(lipid.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
lipid.lme <- lme(Lipid..g.per.cm2.~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(lipid.lme, type=3)
tukey3<- emmeans(lipid.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```

```{r}
summary(lipid.lme)
r.squaredGLMM(lipid.lme)
```
####Coefficients
```{r}
coef(lipid.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
lipidfig<-ggplot(phys, aes(y=Lipid..g.per.cm2., x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Lipids~(g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
lipidfig
```

```{r}
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
lipid_stress_fig<-ggplot(phys_stress, aes(y=Lipid..g.per.cm2., x=Months, color=Bleach, fill=Bleach))+ 
 geom_point(data=phys_stress,aes(y=Lipid..g.per.cm2., x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Lipid..g.per.cm2., x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  #geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
  #geom_point(size=1.5, position= pd)+
  #geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Lipids~(g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
lipid_stress_fig
```
```{r}
library(Rmisc)
lipid_sum<-summarySE(phys, measurevar='Lipid..g.per.cm2.', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
lipid_sum
```

```{r}
lipidfig_3<-ggplot(lipid_sum, aes(y=Lipid..g.per.cm2., x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=lipid_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Lipid..g.per.cm2.-se, ymax=Lipid..g.per.cm2.+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Lipid~(g~'\U2219'~cm^{-2})), limits=c(0,15),breaks=c(0,5,10,15))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
lipidfig_3
```

##TAC
###Normality
```{r}
hist(phys$TAC_CRE.mgprotein.1)
```

```{r}
tac.lm<- lm(TAC_CRE.mgprotein.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(tac.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
tac.lme <- lme(TAC_CRE.mgprotein.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(tac.lme, type=3)
tukey3<- emmeans(tac.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```
```{r}
summary(tac.lme)
r.squaredGLMM(tac.lme)
```
####Coefficients
```{r}
coef(tac.lme)
```

```{r}
tacsum<-summarySE(phys, measurevar = "TAC_CRE.mgprotein.1", groupvars = c("Species", "Months", "Bleach"), na.rm=TRUE, conf.interval = 0.95)
tacsum
```


###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
tacfig<-ggplot(phys, aes(y=TAC_CRE.mgprotein.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
tacfig
```


```{r}
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
tac_stress_fig<-ggplot(phys_stress, aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=TAC_CRE.mgprotein.1, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  #geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
  #geom_point(size=1.5, position= pd)+
  #geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
tac_stress_fig
```
```{r}
library(Rmisc)
tac_sum<-summarySE(phys, measurevar='TAC_CRE.mgprotein.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
tac_sum
```

```{r}
tacfig_3<-ggplot(tac_sum, aes(y=TAC_CRE.mgprotein.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=tac_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=TAC_CRE.mgprotein.1-se, ymax=TAC_CRE.mgprotein.1+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(TAC~(mu~mol~CRE~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
tacfig_3
```


##Citrate synthase
###Normality
```{r}
hist(phys$Citrate.synthase.mU.mg.protein.1)
```

```{r}
cs.lm<- lm(Citrate.synthase.mU.mg.protein.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(cs.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
cs.lme <- lme(Citrate.synthase.mU.mg.protein.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(cs.lme, type=3)
tukey3<- emmeans(cs.lme, list(pairwise ~ Bleach), adjust = "tukey")
tukey3
```

```{r}
summary(cs.lme)
r.squaredGLMM(cs.lme)
```
####Coefficients
```{r}
coef(cs.lme)
```
###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
csfig<-ggplot(phys, aes(y=Citrate.synthase.mU.mg.protein.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_wrap(~Species, scales="free")+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
csfig
```

```{r}
csfig2<-ggplot(phys, aes(y=Citrate.synthase.mU.mg.protein.1, x=Sym.density_10.6cells.cm.2, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="lm")+
  facet_grid(~Species)+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
csfig2 ##this follows the patterns seen in Hawkins et al 2016
```
```{r}
csfig3<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="lm")+
  #geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
  facet_wrap(~Species, scales = "free")+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
csfig3 ##this follows the patterns seen in Hawkins et al 2016
```


```{r}
csfig3<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="lm")+
  #geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
  facet_wrap(~Species, scales = "free")+
  scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
  scale_x_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
csfig3 ##this follows the patterns seen in Hawkins et al 2016
```
```{r}
csfig4<-ggplot(phys, aes(y=Rabs, x=Citrate.synthase.mU.mg.protein.1))+ 
  geom_point(aes(color=Bleach),alpha=0.4)+
  geom_smooth(method="lm",color = 'black',)+
  #geom_hline(yintercept = 0, linetype="solid",  size=0.7, show.legend = TRUE)+
  #facet_wrap(~Species, scales = "free")+
  scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
  scale_x_continuous(expression(CS~Specific~Activity~(mU~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
csfig4 ##this follows the patterns seen in Hawkins et al 2016
```
```{r}
csfigs<-cowplot::plot_grid(csfig4, csfig3, nrow = 1, ncol = 2, rel_heights = c(1,2.5), labels=c('(a)','(b)'))
csfigs
```

```{r}
pd<- position_dodge(0.3)
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
cs_stress_fig<-ggplot(phys_stress, aes(y=Citrate.synthase.mU.mg.protein.1, x=Months, color=Bleach, fill=Bleach))+ 
  geom_boxplot(alpha=0.6)+
  #geom_point(data=phys_stress,aes(y=Protein_mg.cm.2, x=Months, color=Bleach), alpha=0.6)+
  #geom_point(size=1.5, position= pd)+
  #geom_errorbar(aes(ymin=Protein_mg.cm.2-se, ymax=Protein_mg.cm.2+se), stat="identity",width=0.5, position=pd)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(CS~Specific~Activity~(U~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
cs_stress_fig
```
```{r}
library(Rmisc)
cs_sum<-summarySE(phys, measurevar='Citrate.synthase.mU.mg.protein.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
cs_sum
```

```{r}
csfig_3<-ggplot(cs_sum, aes(y=Citrate.synthase.mU.mg.protein.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=cs_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Citrate.synthase.mU.mg.protein.1-se, ymax=Citrate.synthase.mU.mg.protein.1+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
 scale_y_continuous(expression(CS~Specific~Activity~(U~'\U2219'~mg~protein^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
csfig_3
```

```{r}
csfigs<-cowplot::plot_grid(csfig, csfig2, nrow = 2, ncol = 1)
csfigs
```


##Symbiont density
###Normality
```{r}
hist(phys$Sym.density_10.6cells.cm.2)
```

```{r}
sym.lm<- lm(Sym.density_10.6cells.cm.2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(sym.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
sym.lme <- lme(Sym.density_10.6cells.cm.2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(sym.lme, type=3)
tukey3<- emmeans(sym.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```

```{r}
summary(sym.lme)
r.squaredGLMM(sym.lme)
```
####Coefficients
```{r}
coef(sym.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
symfig<-ggplot(phys, aes(y=Sym.density_10.6cells.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})), limits=c(-0,5))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
symfig
```
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
sym_stress_fig<-ggplot(phys_stress, aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach, fill=Bleach))+ 
  geom_point(data=phys_stress,aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Sym.density_10.6cells.cm.2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  geom_boxplot(alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})), limits=c(0,5))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
sym_stress_fig
```

```{r}
library(Rmisc)
sym_sum<-summarySE(phys, measurevar='Sym.density_10.6cells.cm.2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
sym_sum
```

```{r}
symfig_3<-ggplot(sym_sum, aes(y=Sym.density_10.6cells.cm.2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=sym_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "sym", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Sym.density_10.6cells.cm.2-se, ymax=Sym.density_10.6cells.cm.2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Symbiont~density~(10^{6}~cells~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
symfig_3
```

```{r}
lmfig<-ggplot(phys, aes(y=Sym.density_10.6cells.cm.2, x=AFDW_mg.cm.2, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="lm")+
  #facet_grid(~Species)+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
lmfig ##this follows the patterns seen in Hawkins et al 2016
```

##Chlorphyll a
###Normality
```{r}
hist(phys$Chl.a_ug.cm2)
```

```{r}
chla.lm<- lm(Chl.a_ug.cm2~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(chla.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
chla.lme <- lme(Chl.a_ug.cm2~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(chla.lme, type=3)
tukey3<- emmeans(chla.lme, list(pairwise ~ Months), adjust = "tukey")
tukey3
```

```{r}
summary(chla.lme)
r.squaredGLMM(chla.lme)
```
####Coefficients
```{r}
coef(chla.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chlafig<-ggplot(phys, aes(y=Chl.a_ug.cm2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
chlafig
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chla_stress_fig<-ggplot(phys_stress, aes(y=Chl.a_ug.cm2, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=Chl.a_ug.cm2, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Chl.a_ug.cm2, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  geom_boxplot(alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
chla_stress_fig
```

```{r}
library(Rmisc)
chla_sum<-summarySE(phys, measurevar='Chl.a_ug.cm2', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
chla_sum
```

```{r}
chlafig_3<-ggplot(chla_sum, aes(y=Chl.a_ug.cm2, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=chla_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "chla", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Chl.a_ug.cm2-se, ymax=Chl.a_ug.cm2+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
chlafig_3
```

##Chlorphyll a per symbiont
###Normality
```{r}
hist(phys$pg.Chl.a.per.zoox)
```

```{r}
chla.lm<- lm(pg.Chl.a.per.zoox~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(chla.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
chla.lme <- lme(pg.Chl.a.per.zoox~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(chla.lme, type=3)
tukey3<- emmeans(chla.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```
###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chlafig2<-ggplot(phys, aes(y=pg.Chl.a.per.zoox, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})), limits=c(0,50))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
chlafig2
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
chla_stress_fig2<-ggplot(phys_stress, aes(y=pg.Chl.a.per.zoox, x=Months, color=Bleach, fill=Bleach))+ 
  #geom_point(alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  geom_boxplot(alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})), limits=c(0,50))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
chla_stress_fig2
```


```{r}
library(Rmisc)
chlacell_sum<-summarySE(phys, measurevar='pg.Chl.a.per.zoox', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
chlacell_sum
```

```{r}
chlacellfig_3<-ggplot(chlacell_sum, aes(y=pg.Chl.a.per.zoox, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=chlacell_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "chlacell", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=pg.Chl.a.per.zoox-se, ymax=pg.Chl.a.per.zoox+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Chlorophyll~italic(a)~(pg~'\U2219'~cell^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
chlacellfig_3
```


##Melanin

###Normality

```{r}
hist(phys$Melanin_per_tissue)
```
```{r}
mel.lm<- lm(Melanin_per_tissue~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(mel.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
mel.lme <- lme(Melanin_per_tissue~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(mel.lme, type=3)
tukey3<- emmeans(mel.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Months")
tukey3
```

```{r}
summary(mel.lme)
r.squaredGLMM(mel.lme)
```
####Coefficients
```{r}
coef(mel.lme)
```
###Figure

```{r}
#mel$Date<- as.Date(as.POSIXct(mel$Date, origin="1970-01-01"))
melfig<-ggplot(phys, aes(y=Melanin_per_tissue, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Melanin~(mg~melanin~'\U2219'~mg~tissue^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
melfig
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
mel_stress_fig<-ggplot(phys_stress, aes(y=Melanin_per_tissue, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=Melanin_per_tissue, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Melanin_per_tissue, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  geom_boxplot(alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Melanin~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
mel_stress_fig
```

```{r}
library(Rmisc)
mel_sum<-summarySE(phys, measurevar='Melanin_per_tissue', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
mel_sum
```

```{r}
melfig_3<-ggplot(mel_sum, aes(y=Melanin_per_tissue, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=mel_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "mel", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Melanin_per_tissue-se, ymax=Melanin_per_tissue+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Melanin~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(0,0.003))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
melfig_3
```

##PPO

```{r}
ppo<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/PPO all R.csv", strip.white=T)
ppo$Date<- as.Date(ppo$Date, format = "%Y-%m-%d")
ppo$Bleach<-as.factor(ppo$Bleach)
#ppo$Months<-as.factor(ppo$Months)
ppo$Species<-as.factor(ppo$Species)
ppo$Coral_ID<-as.factor(ppo$Coral_ID)
ppo
```
###Normality

```{r}
hist(phys$PPO)
```

```{r}
ppo.lm<- lm(PPO~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(ppo.lm, ask=FALSE, which=1:6)
```

###Stats
```{r}
ppo.lme <- lme(PPO~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(ppo.lme, type=3)
tukey3<- emmeans(ppo.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Months")
tukey3
```
```{r}
summary(ppo.lme)
r.squaredGLMM(ppo.lme)
```
####Coefficients
```{r}
coef(ppo.lme)
```
###Figure

```{r}
#ppo$Date<- as.Date(as.POSIXct(ppo$Date, origin="1970-01-01"))
ppofig<-ggplot(phys, aes(y=PPO, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
ppofig
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
ppo_stress_fig<-ggplot(phys_stress, aes(y=PPO, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=PPO, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=PPO, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  geom_boxplot(alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
ppo_stress_fig
```

```{r}
library(Rmisc)
ppo_sum<-summarySE(phys, measurevar='PPO', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
ppo_sum
```

```{r}
ppofig_3<-ggplot(ppo_sum, aes(y=PPO, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=ppo_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "ppo", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=PPO-se, ymax=PPO+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(0,1.25))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
ppofig_3
```


##Pnet
###Normality
```{r}
hist(phys$Pmax)
```

```{r}
Pnet.lm<- lm(Pmax~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(Pnet.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
Pnet.lme <- lme(Pmax~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(Pnet.lme, type=3)
tukey3<- emmeans(Pnet.lme, list(pairwise ~ Months), adjust = "tukey")
tukey3
tukey3<- emmeans(Pnet.lme, list(pairwise ~Species:Months), adjust = "tukey", simple="Months")
tukey3 #no differences within Species and Bleach 
```
```{r}
summary(Pnet.lme)
r.squaredGLMM(Pnet.lme)
```
####Coefficients
```{r}
coef(Pnet.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
Pnetfig<-ggplot(phys, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
Pnetfig
```


```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
Pnetfig2<-ggplot(phys, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
Pnetfig2
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
pnet_stress_fig<-ggplot(phys_stress, aes(y=Pmax, x=Months, color=Bleach, fill=Bleach))+ 
 geom_point(data=phys_stress,aes(y=Pmax, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=Pmax, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
pnet_stress_fig
```
```{r}
library(Rmisc)
Pnet_sum<-summarySE(phys, measurevar='Pmax', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
Pnet_sum
```

```{r}
Pnetfig_3<-ggplot(Pnet_sum, aes(y=Pmax, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=Pnet_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "Pnet", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=Pmax-se, ymax=Pmax+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Gross~photosynthesis~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(0,4))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
Pnetfig_3
```

##LEDR
###Normality
```{r}
hist(phys$R)
```

```{r}
LEDR.lm<- lm(R~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(LEDR.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
LEDR.lme <- lme(R~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(LEDR.lme, type=3)
tukey3<- emmeans(LEDR.lme, list(pairwise ~ Species:Months), adjust = "tukey", simple="Species")
tukey3
```
```{r}
summary(LEDR.lme)
r.squaredGLMM(LEDR.lme)
```
####Coefficients
```{r}
coef(LEDR.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDRfig<-ggplot(phys, aes(y=R, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
LEDRfig
```


```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDRfig2<-ggplot(phys, aes(y=R, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
LEDRfig2
```


```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
LEDR_stress_fig<-ggplot(phys_stress, aes(y=R, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=R, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=R, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
LEDR_stress_fig
```


```{r}
library(Rmisc)
LEDR_sum<-summarySE(phys, measurevar='R', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
LEDR_sum
```

```{r}
LEDRfig_3<-ggplot(LEDR_sum, aes(y=abs(R), x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=LEDR_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "LEDR", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=abs(R)-se, ymax=abs(R)+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Respiration~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
  #geom_hline(yintercept = 0, size=0.75, color = "black") + 
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
LEDRfig_3
```
##alpha
###Normality
```{r}
hist(phys$alpha)
```

```{r}
alpha.lm<- lm(alpha~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(alpha.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
alpha.lme <- lme(alpha~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(alpha.lme, type=3)
tukey3<- emmeans(alpha.lme, list(pairwise ~ Months), adjust = "tukey")
tukey3
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alphafig<-ggplot(phys, aes(y=alpha, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
alphafig
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alphafig2<-ggplot(phys, aes(y=alpha, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
alphafig2
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
alpha_stress_fig<-ggplot(phys_stress, aes(y=alpha, x=Months, color=Bleach, fill=Bleach))+ 
  #geom_point(alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  geom_boxplot(alpha=0.6,  outlier.shape = NA)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
alpha_stress_fig
```

##P:R
###Normality
```{r}
hist(phys$PR)
```

```{r}
PR.lm<- lm(PR~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(PR.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
PR.lme <- lme(PR~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(PR.lme, type=3)
tukey3<- emmeans(PR.lme, list(pairwise ~ Bleach ), adjust = "tukey")
tukey3
```
```{r}
summary(PR.lme)
r.squaredGLMM(PR.lme)
```
####Coefficients
```{r}
coef(protein.lme)
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
prfig2<-ggplot(phys, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(limits=as.Date(c("2020-08-01","2022-03-15")),date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
prfig2
```

```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
prfig<-ggplot(phys, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
prfig
```
```{r}
library(Rmisc)
PR_sum<-summarySE(phys, measurevar='PR', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
PR_sum
```

```{r}
PRfig_3<-ggplot(PR_sum, aes(y=PR, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=PR_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "PR", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=PR-se, ymax=PR+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
  scale_y_continuous(expression(Photosynthesis:Respiration), limits=c(0,7))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
PRfig_3
```
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PR_stress_fig<-ggplot(phys_stress, aes(y=PR, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=PR, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=PR, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(PPO~activity~(Delta~Abs~490~nm~'\U2219'~mg~protein^{-1}~'\U2219'~min^{-1})), limits=c(-0.1,1.75))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PR_stress_fig
```

```{r}
library(cowplot)
respall<-cowplot::plot_grid(Pnetfig,LEDRfig, nrow=3,ncol=1, align="h", axis = "bt")
respall
```

##PI curves

```{r}
PIOct19<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Oct 2019 PI curve_Teegan.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIOct19$rad<-as.numeric(PIOct19$rad)
PIOct19
```
###Figure - Oct19
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig_Oct19<-ggplot(PIOct19, aes(y=umol.O2.L.hr, x=rad, color=Phenotype, fill=Phenotype))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
  geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") + 
  scale_fill_manual("Phenotype", values=c("Susceptible"= '#DFD3B9',"Resistant"='#796334'))+ #Manually choose the colors
  scale_color_manual("Phenotype", values=c("Susceptible"= '#DFD3B9',"Resistant"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfig_Oct19
```

```{r}
PIOct<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/2021.10.10_KBaypairs_respirometry/Raw_KTB.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIOct$rad<-as.numeric(PIOct$rad)
PIOct
```
###Figure - Oct21
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig<-ggplot(PIOct, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") + 
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfig
```
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig2<-ggplot(PIOct, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+ 
  geom_path()+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfig2
```
```{r}
PIMar<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/March 2022 Respirometry/March22_KTB2.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PIMar$rad<-as.numeric(PIMar$rad)
PIMar
```

###Figure - Mar22
```{r}
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfigmarch<-ggplot(PIMar, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})), limits=c(-2,3))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") + 
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfigmarch
```
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig2<-ggplot(PIMar, aes(y=umol.O2.L.hr, x=rad, color=Bleach, fill=Bleach))+ 
  geom_path()+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfig2
```
```{r}
PISept<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Sept 2022 Respirometry/Sept2022_slopes_raw.csv", stringsAsFactors=FALSE, fileEncoding="latin1")
PISept$rad<-as.numeric(PISept$rad)
PISept$umol.O2.L.hr.cm2<-as.numeric(PISept$umol.O2.L.hr.cm2)
PISept
```
###Figure - Sept22
```{r}
#phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
PIfig3<-ggplot(PISept, aes(y=umol.O2.L.hr.cm2, x=rad, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_continuous(Irradiance~(mu~mol~'\U2219'~m^{-2}~'\U2219'~s^{-1}), limits=c(0,1682))+ 
  scale_y_continuous(expression(Oxygen~evolution~(mu~mol~'\U2219'~h^{-1}~'\U2219'~cm^{-2})),limits=c(-2,3))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  geom_hline(yintercept = 0, linetype = 1, alpha = 0.8, color = "black") + 
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
PIfig3
```

```{r}
library(cowplot)
curves<-cowplot::plot_grid(PIfig_Oct19,PIfig,PIfigmarch, PIfig3, nrow=2,ncol=2, align="h", axis = "bt")
curves
```


##CaCO3 density
###Normality
```{r}
hist(phys$CaCO3.Density_g.mL.1)
```

```{r}
density.lm<- lm(CaCO3.Density_g.mL.1~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(density.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
density.lme <- lme(CaCO3.Density_g.mL.1~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(density.lme, type=3)
tukey3<- emmeans(density.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Months")
tukey3
```
```{r}
summary(density.lme)
r.squaredGLMM(density.lme)
```
####Coefficients
```{r}
coef(density.lme)
```
###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
densityfig<-ggplot(phys, aes(y=CaCO3.Density_g.mL.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1,2.5))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
densityfig
```
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
density_stress_fig<-ggplot(phys_stress, aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach, fill=Bleach))+ 
geom_point(data=phys_stress,aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach), alpha=0.9,position=position_jitterdodge())+
  geom_boxplot(data=phys_stress,aes(y=CaCO3.Density_g.mL.1, x=Months, color=Bleach), alpha=0.5, color="black", outlier.shape = NA)+
  geom_boxplot( alpha=0.6,  outlier.shape = NA, color="black")+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1,2.5))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
density_stress_fig
```
```{r}
library(Rmisc)
density_sum<-summarySE(phys, measurevar='CaCO3.Density_g.mL.1', groupvars=c('Date','Species', 'Bleach'), na.rm=TRUE, conf.interval = 0.95)
density_sum
```

```{r}
densityfig_3<-ggplot(density_sum, aes(y=CaCO3.Density_g.mL.1, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(size=1, position=position_dodge(0.3),stat="identity")+
  #geom_point(data=phys, aes(y=density_mg.cm.2, x=Date), alpha=0.4)+
  #geom_smooth(method="gam", formula = y ~ s(x, bs = "density", k=3), se=F)+
  facet_wrap(~Species)+
  geom_linerange(aes(ymin=CaCO3.Density_g.mL.1-se, ymax=CaCO3.Density_g.mL.1+se), width= 0.7,  position=position_dodge(0.3),stat="identity") +
  geom_path(aes(group = interaction(Bleach), stat="identity"), position=position_dodge(0.3), linetype="solid")+
  scale_x_date(breaks = as.Date(c("2019-10-01","2020-02-01","2020-06-01","2020-10-01","2021-02-01","2021-06-01","2021-10-01","2022-02-01","2022-06-01","2022-10-01")), date_labels = "%b %Y")+ 
 scale_y_continuous(expression(CaCO[3]~density~(g~'\U2219'~mL^{-1})), limits=c(1.2,2.2))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(angle=90,vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12,face="italic"))
densityfig_3
```
##Internal volume
###Normality
```{r}
hist(phys$X.internal.volume)
```

```{r}
intvol.lm<- lm(X.internal.volume~Species*Bleach*Months, data=phys) #Gaussian
par(mfrow=c(2,3))
plot(intvol.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
intvol.lme <- lme(X.internal.volume~Species*Bleach*Months, random = ~1|Coral_ID, data=phys, na.action=na.exclude)
car::Anova(intvol.lme, type=3)
tukey3<- emmeans(intvol.lme, list(pairwise ~ Species:Bleach:Months), adjust = "tukey", simple="Bleach")
tukey3
```

###Figure
```{r}
phys$Date<- as.Date(as.POSIXct(phys$Date, origin="1970-01-01"))
intvolfig<-ggplot(phys, aes(y=X.internal.volume, x=Date, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.4)+
  geom_smooth(method="gam", formula = y ~ s(x, bs = "cs", k=3))+
  #geom_boxplot(aes(group = interaction(Date,Bleach), stat="identity"), alpha=0.7,  outlier.shape = NA)+
  facet_grid(~Species)+
  scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  scale_y_continuous(expression(Internal~volume~("%")))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12, angle=90),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
intvolfig
```
```{r}
library(cowplot)
allphys<-cowplot::plot_grid(proteinfig_3,lipidfig_3,AFDWfig_3,densityfig_3,ppofig_3,melfig_3, symfig_3,chlafig_3,chlacellfig_3, Pnetfig_3, LEDRfig_3,PRfig_3,nrow=4, ncol=3,  align="h", axis = "bt")
allphys
```
```{r}
library(cowplot)
allphyssupp<-cowplot::plot_grid(tacfig_3,csfig_3,ppofig_3,melfig_3, chlacellfig_3,tacfig_3,csfig_3,ppofig_3,melfig_3, chlacellfig_3,melfig_3, chlacellfig_3,nrow=4, ncol=3,  align="h", axis = "bt")
allphyssupp
```

```{r}
library(cowplot)
phys2<-plot_grid(proteinfig,symfig, nrow=2, ncol=1,  align="h", axis = "bt")
phys2
```
#Composite Figure
```{r}
library(cowplot)
allphys_stress<-cowplot::plot_grid(AFDW_stress_fig,protein_stress_fig,lipid_stress_fig, density_stress_fig,sym_stress_fig,chla_stress_fig,tac_stress_fig,mel_stress_fig,ppo_stress_fig,pnet_stress_fig,LEDR_stress_fig,PR_stress_fig, nrow=4, ncol=3,  align="h", axis = "bt")
allphys_stress
```

```{r}
library(cowplot)
allphys_stress<-cowplot::plot_grid(proteinfig,AFDWfig,lipidfig,densityfig,symfig,chlafig,tacfig,ppofig,csfig,Pnetfig_3,LEDRfig_3,PRfig_3, nrow=4, ncol=3,  align="h", axis = "bt")
allphys_stress
```

##Multivariate 

```{r}
phys<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Phys data with Teegan MDS no Oct-Nov 2020 and only peak heatwave.csv", strip.white=T)
phys$Date<- as.Date(phys$Date, format = "%Y-%m-%d")
phys$Bleach<-as.factor(phys$Bleach)
phys$Months<-as.factor(phys$Months)
phys$Coral<-as.factor(phys$Coral)
phys$Coral_ID<-as.factor(phys$Coral_ID)
phys
```
```{r}
library(lubridate)
library(dplyr)
#grouping each June-March; Jan-Mar "recovery"; June to June calendar year; heat stress (date when it falls below MMM) define this as recovery; bleaching remains Jan/Feb
phys$day <- day(as.POSIXlt(phys$Date))
phys$month <- month(as.POSIXlt(phys$Date))
phys$year <- year(as.POSIXlt(phys$Date))
phys$year<-as.factor(phys$year)
phys<-phys%>%
  mutate(season= ifelse (month %in% c(5,6,7,8,9,10), "summer",
                         ifelse(month %in% c(11,12,1,2,3,4), "winter", NA))) %>%
  mutate(period= ifelse(year %in% c(2019) & month %in% c(9,10,11,12), "A",
                         ifelse(year %in% c(2019) & month %in% c(5,6,7,8), "A",
                                 ifelse(year %in% c(2020) & month %in% c(1,2,3,4), "A",
                                 ifelse(year %in% c(2020) & month %in% c(5,6,7,8,9,10,11,12), "B",
                                 ifelse(year %in% c(2021) & month %in% c(1,2,3,4), "B",
                                 ifelse(year %in% c(2021) & month %in% c(5,6,7,8,9,10,11,12),"C",
                                 ifelse(year %in% c(2022) & month %in% c(1,2,3,4), "C",NA))))))))
phys
```
```{r}
#phys<-filter(phys, Period == c("Recovery"))
#phys
```

```{r}
unique(phys$Period)
```

```{r}
colnames(phys)
```

```{r}
library(vegan)
phys.rda<- rda(phys[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)
```

```{r}
biplot(phys.rda, scaling=1, main='Scaling')
```

```{r}
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, phys)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scores
```
```{r}
include_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]
```

```{r}
g<-ggplot()+
  geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
  facet_wrap(~Coral)+
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") + 
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
  geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
  geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
  scale_color_brewer(palette = "RdYlBu")+
  #scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors   
  scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
  scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
  scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
g
```
```{r}
library(cowplot)
pcaillustrator<-cowplot::plot_grid(g,g,g, nrow=3, align="h", axis = "bt")
pcaillustrator
```

```{r}
eig<-eigenvals(phys.rda)
eig
```
```{r}
veg.hull= pca.sites.scores %>% group_by(Months) %>%
  do({
    x=.
    x[chull(x$PC1, x$PC2),]
  })
```

```{r}
g+ geom_polygon(data=veg.hull, aes(y=PC2, x=PC1,fill=Months), alpha=0.2)+
  scale_fill_brewer(palette = "RdYlBu")
```

###MDS Montipora only
```{r}
mdsmon<-dplyr::filter(phys, Coral== c("Montipora capitata"))
colnames(mdsmon)
#row.has.na <- apply(mdsbefore[,(8:17)], 1, function(x){any(is.na(x))})
#mdsbefore.filtered <- mdsbefore[!row.has.na,]
#mdsbefore.filtered
```
```{r}
library(vegan)
phys.rda<- rda(mdsmon[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)
```

```{r}
biplot(phys.rda, scaling=1, main='Scaling')
```

```{r}
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, mdsmon)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scores
```
```{r}
include_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]
```

```{r}
gmon<-ggplot()+
  geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
  facet_wrap(~Coral)+
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") + 
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
  geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
  geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
  scale_color_brewer(palette = "RdYlBu")+
  #scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors   
  scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
  scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
  scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
gmon
```

```{r}
gmonseason<-ggplot()+
  geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=season, shape=Bleach), size=3, alpha=0.8)+
  facet_wrap(~Coral)+
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") + 
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
  geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
  geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
  #scale_color_brewer(palette = "RdYlBu")+
  scale_color_manual("season", values=c("summer"='indianred3', "winter"= "navyblue","NA"="white"))+
  #scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors   
  scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
  scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
  scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
gmonseason
```

```{r}
library(cowplot)
pcaillustrator<-cowplot::plot_grid(gmon,gpor,gmonseason, gporseason, nrow=2, align="h", axis = "bt")
pcaillustrator
```

```{r}
eig<-eigenvals(phys.rda)
eig
```
```{r}
veg.hull= pca.sites.scores %>% group_by(Months) %>%
  do({
    x=.
    x[chull(x$PC1, x$PC2),]
  })
```

###MDS Porites only
```{r}
mdspor<-dplyr::filter(phys, Coral== c("Porites compressa"))
colnames(mdspor)
#row.has.na <- apply(mdsbefore[,(8:17)], 1, function(x){any(is.na(x))})
#mdsbefore.filtered <- mdsbefore[!row.has.na,]
#mdsbefore.filtered
```
```{r}
library(vegan)
phys.rda<- rda(mdspor[,(7:13)], na.rm=TRUE, scale=TRUE)#include only columns here that are benthic categories (e.g, CCA, macroalgae, Porites)
```

```{r}
biplot(phys.rda, scaling=1, main='Scaling')
```

```{r}
pca.sites.scores<- as.data.frame(scores(phys.rda, display='sites'))
pca.sites.scores<- data.frame(pca.sites.scores, mdspor)
pca.species.scores<- as.data.frame(scores(phys.rda, display='species'))
pca.species.scores$Species<- rownames(pca.species.scores)
pca.species.scores
```
```{r}
include_list<- c("Protein_mg.cm.2","Sym.density_10.6cells.cm.2","Chl.a_ug.cm2", "pg.Chl.a.per.zoox", "AFDW_mg.cm.2", "CaCO3.Density_g.mL.1") #List of vectors to inclue on the below plot
pca.species.scores<-pca.species.scores[include_list,]
```

```{r}
eig<-eigenvals(phys.rda)
eig
```

```{r}
gpor<-ggplot()+
  geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=Months, shape=Bleach), size=3, alpha=0.8)+
  facet_wrap(~Coral)+
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") + 
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
  geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
  geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
  scale_color_brewer(palette = "RdYlBu")+
  #scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors   
  scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
  scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
  scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
gpor
```
```{r}
gporseason<-ggplot()+
  geom_point(data=pca.sites.scores, aes(y=PC2, x=PC1, color=season, shape=Bleach), size=3, alpha=0.8)+
  facet_wrap(~Coral)+
  geom_hline(yintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") + 
  geom_vline(xintercept = 0, linetype = 2, alpha = 0.8, color = "darkgray") +
  geom_segment(data=pca.species.scores, aes(y=0, x=0, yend=PC2, xend=PC1), arrow=arrow(length=unit(0.3, 'lines')),color='black', linetype='solid',alpha=0.9)+
  geom_text(data=pca.species.scores, aes(y=PC2, x=PC1, label=Species), color="black")+
  #scale_color_brewer(palette = "RdYlBu")+
  scale_color_manual("season", values=c("summer"='indianred3', "winter"= "navyblue","NA"="white"))+
  #scale_color_manual("Year", values=c("2019"='coral2',"2020"='paleturquoise2',"2021"='darkslategray4'))+ #Manually choose the colors   
  scale_shape_manual("Bleach", values=c("Bleach"=(pch=8),"Non-bleach"=(pch=16)))+ #Manually choose the colors
  scale_x_continuous(limits=c(-3,3),paste(names(eig[1]), sprintf('(%0.1f%% explained var.)', 100 * eig[1]/sum(eig))))+
  scale_y_continuous(paste(names(eig[2]), sprintf('(%0.1f%% explained var.)', 100 * eig[2]/sum(eig))))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
gporseason
```




```{r}
permanova_por<-adonis(mdspor[,(7:13)] ~ Bleach*Months, data=mdspor, permutations=9999)
permanova_por
library(pairwiseAdonis)
pairwise.adonis2(mdspor[,(7:13)] ~Months, data=mdspor, permutations = 9999, na.rm=T)
```

```{r}
library(cowplot)
pcaillustrator<-cowplot::plot_grid(gmon,gpor,g, nrow=3,ncol=2, align="h", axis = "bt")
pcaillustrator
```

#STHS
##Temperature data
```{r}
amb<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/AMB_21257937.csv")
mild<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/3C_21257935.csv")
mod<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/6C_21257936.csv")
ex<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/STHS temperature profiles/9C_20473299.csv")
amb<- plyr::rename(amb, c("ï..Date"="Date"))
amb$Date<-as.Date(amb$Date)
amb$Treatment<-as.factor(amb$Treatment)
amb
mild<- plyr::rename(mild, c("ï..Date"="Date"))
mild$Date<-as.Date(mild$Date)
mild$Treatment<-as.factor(mild$Treatment)
mild
mod<- plyr::rename(mod, c("ï..Date"="Date"))
mod$Date<-as.Date(mod$Date)
mod$Treatment<-as.factor(mod$Treatment)
mod
ex<- plyr::rename(ex, c("ï..Date"="Date"))
ex$Date<-as.Date(ex$Date)
ex$Treatment<-as.factor(ex$Treatment)
ex
```

```{r}
alltemp<- merge(amb, mild, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp<- merge(alltemp, mod, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp<- merge(alltemp, ex, by=c("Date","Time","Temperature","Treatment"), all=T)
alltemp$Date_Time<- as.POSIXct(paste(alltemp$Date, alltemp$Time), "%Y-%m-%d hh:mm:ss")
alltemp$Treatment<-as.factor(alltemp$Treatment)
alltemp$hour <- as.POSIXlt(alltemp$Date_Time)$hour
alltemp
unique(alltemp$hour)
```
```{r}
#write.csv(alltemp, "Short-term heat stress temperature data.csv")
```


```{r}
tempsub<-filter(alltemp, Date == c("2022-09-01", "2022-09-02","2022-09-03"))
tempsub
```

```{r}
tempsub_mean<-summarySE(tempsub, measurevar='Temperature', na.rm=TRUE, conf.interval = 0.95)
tempsub_mean
```

```{r}
alltemp_mean<-summarySE(alltemp, measurevar='Temperature', groupvars=c('Treatment', "Date", "hour"), na.rm=TRUE, conf.interval = 0.95)
alltemp_mean
```




```{r}
sths.lm<- lm(Temperature~Treatment, data=alltemp_mean) #Gaussian
car::Anova(sths.lm)
tukey3<- emmeans(sths.lm, list(pairwise ~ Treatment), adjust = "tukey")
tukey3
par(mfrow=c(2,3))
plot(sths.lm, ask=FALSE, which=1:6)
```



```{r}
lims <- as.POSIXct(strptime(c("2022-09-04 00:00", "2022-09-05 0:00"), 
                   format = "%Y-%m-%d %H:%M"))
alltemp$Date<- as.Date(as.POSIXct(alltemp$Date, origin="1970-01-01"))
STHS_hobo_temp<-ggplot(alltemp, aes(y=Temperature, x=Date_Time, color=Treatment))+
  geom_line(size=1)+
  #geom_hline(yintercept = 27.7, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
  geom_hline(yintercept = 28.7, linetype="solid", color = 'black', size=0.7, show.legend = TRUE)+
  scale_x_datetime(labels = date_format("%H:%M"), breaks = date_breaks("3 hours"),limits=lims,  expand=c(0.015,0.015))+
  scale_y_continuous(expression(Temperature~(degree~C)))+
  scale_color_brewer(palette ="RdBu", direction =-1)+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
        plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
        panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
        strip.background = element_blank(), 
        #strip.text = element_blank(),
        legend.title = element_text(),
        legend.position=c(0.89,0.80),
        axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger 
        axis.title.x = element_blank(),#making the axis title larger 
        axis.title.y = element_text(size=12))#making the axis title larger 
STHS_hobo_temp
```
```{r}
tempfigs<-cowplot::plot_grid(STHS_hobo_temp, STHS_hobo_temp,STHS_hobo_temp, STHS_hobo_temp, nrow = 2, ncol = 2)
tempfigs
```

##PAM
```{r}
pam<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/PAM data for STHS.csv")
pam$Treatment<- as.factor(pam$Treatment)
pam$Bleach<-as.factor(pam$Bleach)
#pam$Months<-as.factor(pam$Months)
pam$Species<-as.factor(pam$Species)
pam$Colony.ID<-as.factor(pam$Colony.ID)
pam$Rep<-as.factor(pam$Rep)
pam$Temperature<- as.numeric(pam$Temperature)
pam
```
```{r}
library(Rmisc)
allpamsum<-summarySE(pam, measurevar='Y', groupvars=c('Treatment',"Temperature",'Species','Bleach',"Colony.ID"), na.rm=TRUE, conf.interval = 0.95)
allpamsum
```


###Normality
```{r}
hist(allpamsum$Y)
```

```{r}
sths.lm<- lm(Y~Treatment*Species*Bleach, data=allpamsum) #Gaussian
par(mfrow=c(2,3))
plot(sths.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
Y.lme <- lme(Y~Treatment*Species*Bleach, random = ~1|Colony.ID, data=allpamsum, na.action=na.exclude)
car::Anova(Y.lme, type=3)
tukey3<- emmeans(Y.lme, list(pairwise ~ Treatment:Species), adjust = "tukey", simple="Species")
tukey3
tukey2<- emmeans(Y.lme, list(pairwise ~ Treatment:Bleach), adjust = "tukey", simple="Bleach")
tukey2
```

```{r}
summary(Y.lme)
r.squaredGLMM(Y.lme)
```
####Coefficients
```{r}
coef(Y.lme)
```

```{r}
allpamsum2<-summarySE(pam, measurevar='Y', groupvars=c('Treatment',"Temperature",'Species','Bleach'), na.rm=TRUE, conf.interval = 0.95)
allpamsum2
```
###Figure
```{r}
allpamsum$Treatment <- factor(allpamsum$Treatment, levels=c("AMB","3C","6C","9C"))
allpamsum$Temperature<- factor(allpamsum$Temperature, levels =c("27.7","30.7","33.7","36.7"))
allpamsum$Bleach<- factor(allpamsum$Bleach, levels =c("Non-bleach","Bleach"))
allpamsum2$Treatment <- factor(allpamsum2$Treatment, levels=c("AMB","3C","6C","9C"))
allpamsum2$Temperature<- factor(allpamsum2$Temperature, levels =c("27.7","30.7","33.7","36.7"))
allpamsum2$Bleach<- factor(allpamsum2$Bleach, levels =c("Non-bleach","Bleach"))
pamfig<-ggplot(allpamsum2, aes(y=Y, x=Treatment, color=Bleach))+ 
  geom_point(data=allpamsum, aes(y=Y,x=Treatment, color=Bleach),alpha=0.5,position=position_jitterdodge(0.05))+
  geom_path(aes(stat="identity"), position=position_dodge(0.5))+
  facet_wrap(~Species, nrow=1)+
  geom_point(size=1, position=position_dodge(0.5),stat="identity")+
  geom_errorbar(aes(ymin=Y-se, ymax=Y+se, width= 0.5),  position=position_dodge(0.5),stat="identity") +
  scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.50,0.75))+  
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_blank(),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12, face="italic"))
pamfig
```
```{r}
ed50m<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Montipora ed50.csv")
ed50m$Bleach<-as.factor(ed50m$Bleach)
ed50m
```

```{r}
ed50p<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Porites ed50.csv")
ed50p$Bleach<-as.factor(ed50p$Bleach)
ed50p
```

```{r}
allpamsumporites<-filter(allpamsum, Species == "Porites compressa")
allpamsummontipora<-filter(allpamsum, Species == "Montipora capitata")
```

#Porites DRM model
```{r}
library(drc) #if not working, ensure temperature is numeric
sths.drc.por <- drm(Y~Temperature, fct=LL.3(),
                          data = allpamsumporites,
                          curveid = Bleach)
sths.drc.por2 <- drm(Y~Temperature, fct=L.3(),
                          data = allpamsumporites,
                          curveid = Bleach)
summary(sths.drc.por)# run model.
plot(sths.drc.por)
ed50<-ED(sths.drc.por, 50, interval="delta")
ed50
```


```{r}
AICc(sths.drc.por, sths.drc.por2)
```

```{r}
##Create predictions data frame
newdata = with(allpamsumporites, 
                       expand.grid(Bleach = levels(Bleach),
                                 Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.por, newdata=newdata, interval = "confidence", level=0.95))
#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>% 
  group_by(Bleach,Temperature) %>% 
  summarise_all(.funs=mean)
pred.average
```

```{r}
pam.fig.por<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
  annotate("rect",xmin=36.94588, xmax=37.41424, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
  annotate("rect", xmin=37.01656, xmax=37.53534,ymin=-Inf, ymax=Inf,  fill= "#796334",  alpha = 0.1) +
  geom_line(size=1)+
  geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.4, show.legend = FALSE) +
  geom_point(data=allpamsumporites, aes(y=Y, x=Temperature, color=Bleach),alpha=0.7,position=position_jitterdodge(0.05))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.5,0.75))+  
  geom_vline(xintercept = 37.180062, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
  geom_vline(xintercept = 37.27595, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
  #geom_point(data = ed50p, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
pam.fig.por
```




```{r}
library(drc)
sths.drc.mon <- drm(Y~Temperature, fct=LL.3(),
                          data = allpamsummontipora,
                          curveid = Bleach)
summary(sths.drc.mon)# run model.
plot(sths.drc.mon)
ed50<-ED(sths.drc.mon, 50, interval="delta")
ed50
```
```{r}
##Create predictions data frame
newdata = with(allpamsummontipora, 
                      expand.grid(Bleach = levels(Bleach),
                                 Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.mon, newdata=newdata, interval = "confidence", level=0.95))
#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>% 
  group_by(Bleach,Temperature) %>% 
  summarise_all(.funs=mean)
pred.average
```
```{r}
pam.fig.mon<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+ 
  annotate("rect",xmin=35.92488, xmax=36.27658, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
  annotate("rect", xmin=36.47089, xmax=36.74191,ymin=-Inf, ymax=Inf,  fill= "#796334",  alpha = 0.1) +
  geom_line(size=1)+
  geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.4, show.legend = FALSE) +
  geom_point(data=allpamsummontipora, aes(y=Y, x=Temperature, color=Bleach),alpha=0.7,position=position_jitterdodge(0.05))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.75), breaks=c(0,0.25,0.5,0.75))+ 
  geom_vline(xintercept = 36.100733, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
  geom_vline(xintercept = 36.606397, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
  #geom_point(data = ed50m, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.2),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
pam.fig.mon
```

```{r}
pamfig2<-ggplot(allpamsum, aes(y=Y, x=Temperature, color=Bleach, fill=Bleach))+ 
  geom_point(alpha=0.5)+
  geom_smooth(method=drm, method.args=list(fct=L.3()), se=F)+
  facet_grid(~Species)+
  #scale_x_date(date_breaks = "4 months", date_labels = "%b %y")+ 
  #scale_y_continuous(expression(Chlorophyll~italic(a)~(mu~g~'\U2219'~cm^{-2})))+
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_y_continuous(expression(Photosynthetic~efficiency~(Fv/Fm)), limits=c(0,0.8), breaks=c(0,0.25,0.50,0.75))+ 
  #geom_hline(yintercept=0.4)+
  geom_vline(xintercept =c(36.23238), linetype='solid', size=1, color='#DFD3B9')+
  geom_vline(xintercept =c(37.08728), linetype='dashed', size=1, color='#DFD3B9')+
  geom_vline(xintercept =c(36.622434), linetype='solid', size=1, color='#796334')+
  geom_vline(xintercept =c(37.185249), linetype='dashed', size=1, color='#796334')+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.12,0.15),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(size=12, face="italic"))
pamfig2
```


```{r}
pamfigs<-cowplot::plot_grid(pamfig2, pamfig2, nrow = 2, ncol = 1)
pamfigs
```

##Color score
```{r}
color<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Color score data STHS.csv")
color$Treatment<- as.factor(color$Treatment)
color$Bleach<-as.factor(color$Bleach)
#color$Months<-as.factor(color$Months)
color$Species<-as.factor(color$Species)
color$Colony.ID<-as.factor(color$Colony.ID)
#color$Rep<-as.factor(color$Rep)
color
```

###Normality
```{r}
hist(color$Color_avg)
```

```{r}
sthsc.lm<- lm(Color_avg~Treatment*Species*Bleach, data=color) #Gaussian
par(mfrow=c(2,3))
plot(sthsc.lm, ask=FALSE, which=1:6)
```
###Stats
```{r}
color.lme <- lme(Color_avg~Treatment*Species*Bleach, random = ~1|Colony.ID, data=color, na.action=na.exclude)
car::Anova(color.lme, type=3)
tukey3<- emmeans(color.lme, list(pairwise ~ Species:Bleach), adjust = "tukey", simple="Bleach")
tukey3
tukey2<- emmeans(color.lme, list(pairwise ~ Treatment), adjust = "tukey")
tukey2
```
```{r}
summary(color.lme)
r.squaredGLMM(color.lme)
```
####Coefficients
```{r}
coef(color.lme)
```

```{r}
allcolorsumporites<-filter(color, Species == "Porites compressa")
allcolorsumporites
allcolorsummontipora<-filter(color, Species == "Montipora capitata")
allcolorsummontipora
```

#Porites DRM model
```{r}
library(drc)
sths.drc.por <- drm(Color_avg~Temperature, fct=LL.3(),
                          data = allcolorsumporites,
                          curveid = Bleach)
sths.drc.por2 <- drm(Color_avg~Temperature, fct=L.3(),
                          data = allcolorsumporites,
                          curveid = Bleach)
summary(sths.drc.por)# run model.
plot(sths.drc.por)
ed50<-ED(sths.drc.por, 50, interval="delta")
ed50
```


```{r}
AICc(sths.drc.por, sths.drc.por2)
```

```{r}
##Create predictions data frame
newdata = with(allcolorsumporites, 
                       expand.grid(Bleach = levels(Bleach),
                                 Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.por, newdata=newdata, interval = "confidence", level=0.95))
#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>% 
  group_by(Bleach,Temperature) %>% 
  summarise_all(.funs=mean)
pred.average
```
```{r}
ed50p<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Porites ed50 color.csv")
ed50p$Bleach<-as.factor(ed50m$Bleach)
ed50p
```

```{r}
color.fig.por<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+
  annotate("rect",xmin=33.8304, xmax=34.93152, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
  annotate("rect", xmin=34.45524, xmax=34.7909, ymin=-Inf, ymax=Inf,  fill= "#796334",  alpha = 0.1) +
  geom_line(size=1)+
  geom_point(data=allcolorsumporites, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
  geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
  #geom_segment(data = ed50p, aes(y=Estimate,yend=-0.1, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = 1.5)+
  #geom_point(data = ed50p, aes(y=Estimate, x = ed50),size=3)+
  #geom_point(size=1, position=position_dodge(0.5),stat="identity")+
  #geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5),  position=position_dodge(0.5),stat="identity") +
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  #scale_y_continuous(expression(Color~score),limits=c(-.25,1.1), breaks=c(-0.25,0,.25,.5,.75,1.0))+  
  geom_vline(xintercept = 34.62307, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
  geom_vline(xintercept = 34.38096, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
  #geom_point(data = ed50p, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
color.fig.por
```
```{r}
color.fig.por2<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+ 
  geom_line(size=1)+
  #geom_segment(data = ed50p, aes(y=Estimate,yend=0, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = .5)+
  #geom_point(data = ed50p, aes(y=Estimate, x = ed50),size=1)+
  geom_point(data=allcolorsumporites, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
  #geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
  #geom_point(size=1, position=position_dodge(0.5),stat="identity")+
  #geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5),  position=position_dodge(0.5),stat="identity") +
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  scale_y_continuous(expression(Color~score))+  
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position="none",
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
color.fig.por2
```

```{r}
library(drc)
sths.drc.mon <- drm(Color_avg~Temperature, fct=LL.3(),
                          data = allcolorsummontipora,
                          curveid = Bleach)
summary(sths.drc.mon)# run model.
plot(sths.drc.mon)
ed50<-ED(sths.drc.mon, 50, interval="delta")
ed50
```
```{r}
##Create predictions data frame
newdata = with(allcolorsummontipora, 
                      expand.grid(Bleach = levels(Bleach),
                                 Temperature=seq(min(Temperature, na.rm=TRUE), max(Temperature, na.rm=TRUE)+ 1, 0.1)))
pred<- as.data.frame(predict(sths.drc.mon, newdata=newdata, interval = "confidence", level=0.95))
#newdata = data.frame(newdata, fvfm = newdata$Prediction, Lower = newdata$Lower, Upper = newdata$Upper)
pred$Bleach = newdata$Bleach
pred$Temperature = newdata$Temperature
pred.average = pred %>% 
  group_by(Bleach,Temperature) %>% 
  summarise_all(.funs=mean)
pred.average
```

```{r}
ed50m<-read.csv("/Users/imkri/Desktop/Penn Postdoc/Hawaii/Montipora ed50 color.csv")
ed50m$Bleach<-as.factor(ed50m$Bleach)
ed50m
```


```{r}
color.fig.mon<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+ 
  #geom_segment(data = ed50m, aes(y=Estimate,yend=-.10, xend=ed50, x = ed50, color=Bleach),linetype = 1, size =1.5)+
  geom_line(size=1)+
  annotate("rect",xmin=33.78391, xmax=34.65903, ymin=-Inf, ymax=Inf,fill ="#DFD3B9", alpha = 0.2)+
  annotate("rect", xmin=34.1545, xmax=34.91972, ymin=-Inf, ymax=Inf,  fill= "#796334",  alpha = 0.1) +
  geom_point(data=allcolorsummontipora, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
  geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
  #geom_point(size=1, position=position_dodge(0.5),stat="identity")+
  #geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5),  position=position_dodge(0.5),stat="identity") +
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  scale_y_continuous(expression(Color~score),limits=c(-.25,1.1),breaks=c(-0.25,0,.25,.5,.75,1.0))+  
  geom_vline(xintercept = 34.22147, linetype = 2, size=1, alpha = 0.8, color = "#DFD3B9") +
  #geom_rect(aes(xmin=33.34961, xmax=35.09332, ymin=Inf, ymax=Inf), alpha = 0.8,color = "#DFD3B9",fill = "#DFD3B9")+
  geom_vline(xintercept = 34.53711, linetype = 2, size=1,alpha = 0.8, color = "#796334") +
  #geom_point(data = ed50m, aes(y=Estimate, x = ed50,color=Bleach,fill=Bleach),size=4, shape=17)+
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.2),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
color.fig.mon
```

```{r}
color.fig.mon2<-ggplot(pred.average, aes(y=Prediction, x=Temperature, color=Bleach, fill=Bleach))+ 
  geom_line(size=1)+
  #geom_segment(data = ed50m, aes(y=Estimate,yend=0, xend=ed50, x = ed50, color=Bleach),linetype = 1, size = 2)+
  #geom_point(data = ed50m, aes(y=Estimate, x = ed50),size=3)+
  geom_point(data=allcolorsummontipora, aes(y=Color_avg, x=Temperature, color=Bleach),alpha=0.3,position=position_jitterdodge(0.05))+
  #geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = Bleach), alpha = 0.5, show.legend = FALSE) +
  #geom_point(size=1, position=position_dodge(0.5),stat="identity")+
  #geom_errorbar(aes(ymin=Prediction-Lower, ymax=Prediction+Upper, width= 0.5),  position=position_dodge(0.5),stat="identity") +
  scale_fill_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+ #Manually choose the colors
  scale_x_continuous(expression(Temperature~(degree~C)), limits=c(27,38),breaks=c(27,29,31,33,35,37))+
  scale_y_continuous(expression(Color~score))+  
  #scale_color_manual("Bleach", values=c("Bleach"= '#DFD3B9',"Non-bleach"='#796334'))+
  theme_classic()+
  theme(axis.text.x=element_text(vjust=0.5, size=12),
        axis.text.y=element_text(vjust=0.5, size=12),
        axis.title.x=element_text(size=12),
        axis.title.y=element_text(size=12),
        legend.text = element_text(vjust=0.5, size=12),
        legend.position=c(0.15,0.2),
        panel.background= element_rect(fill=NA, color='black'),
        strip.text = element_text(vjust=0.5, size=12))
color.fig.mon2
```

```{r}
colorfigs<-cowplot::plot_grid(color.fig.mon, color.fig.por, nrow = 1, ncol = 2)
colorfigs
```
```{r}
colorfigs2<-cowplot::plot_grid(color.fig.mon2, color.fig.por2, nrow = 1, ncol = 2)
colorfigs2
```

```{r}
hobo2<-cowplot::plot_grid(STHS_hobo_temp,STHS_hobo_temp, nrow = 2, ncol = 1)
hobo2
```


```{r}
pamcolorfigsall<-cowplot::plot_grid(pam.fig.mon,pam.fig.por, color.fig.mon, color.fig.por,pam.fig.mon,pam.fig.por, color.fig.mon, color.fig.por,nrow = 4, ncol = 3)
pamcolorfigsall
```

```{r}
pamcolorfigswithtemp<-cowplot::plot_grid(STHS_hobo_temp,pamcolorfigsall,nrow = 1, ncol = 2, rel_widths = c(1,2))
pamcolorfigswithtemp
```
